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I'm studying about strict binary tree topologies and I found a way to check how many possible topologies it is possible to build given n number of leaves of the tree. The equation for this calculation is as follows:
However, this above equation returns the number of possible topologies given n, including mirrored trees. I need to know the amount of possible non-mirrored topologies.
I found a very interesting article (below) that seems to show the calculation of number of possible topologies given n for non-mirrored trees, but I didn't understand how to calculate it. Can anyone help, showing in practice for n = 10 and n = 11? Thank you very much and sorry for my bad english.
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Thank you very much for answering!
Sorry for not being clear in my question.
"I would imagine you mean directed rooted trees where every node has two or zero children."
YES!
"And I think you mean by "topology" an isomorphism class, where an isomorphism of trees is a relabelling of nodes that preserves (and reflects, since the inverse is an isomorphism too) edges."
NO!
I mean a mirroed topology (isomorfism) as being fliped in a flat surface without changing its leaf nodes labelling. Visualy it's same isomorfism but when coding it for matematical propourses, it produces different codes.
An example of mirrored strict binary tree:
Again: My doubt is how to use given math expression below to calculating the number of possible topologies of a binary strict tree. For n = 10 and n = 11 (n is the number of leaves of the tree)
Or we can forget all the context. What I really don't understand is how to mathematically calculate n = 10 and n = 11 (for example) using that expression below.
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Dear all,
I have been finding several published papers on soft set, soft topology and hybrid structures. In early days of my career in soft topology, I also worked with notions of Cagman et al., Shabir and Naz, etc. But, I must admit boldly that ideas of soft set theory, soft topology, etc. defined by others are incorrect. Prof. Molodtsov raised questions many times on available notions of soft empty set, soft absolute set, etc. He showed disagreements on these notions which carry no sense of soft set in reality. Prof. Molodtsov had disagreements on operations of soft sets, soft mappings, etc. His arguments and disagreements were published in several journals, but I am sad to say that soft set researchers community never tried to find Prof. Molodtsov, the father of soft set, along with his works on soft sets.
Thus, I am bold enough to ask following questions to researchers of soft topology:
1) How can you claim that you are following correct notions and meanings of soft topology?
2) Have you ever tried enough to search about Prof. Molodtsov and his published papers post 1999's soft set theory before publishing rubbish ideas in spite of the fact that Prof. Molodtsov showed us correct path in soft set, soft topology, soft rational analysis, etc.? The published papers of others are not contributing any correct idea to soft set theory and hybrid structures by anyway. These papers are simply misleading young researchers because of some arrogant researchers of soft set theory who are desperately ready to reject ideas and advices of Prof. Molodtsov, the father of soft set theory just for publication bof their ideas or to increase citations.
Thus, I request editors of journals to stop publishing incorrect ideas of soft set theory. I also request publishing houses to encourage correct notions and ideas of soft set theory and hybrid structures. I also request American Mathematical Society, European Mathematical Society, etc. to take initiative to organise conferences on soft set theory for the discussion of correct structures of soft set, soft topology, etc. I am available for debates on correct structures of soft set theory and related ideas in international conferences if one is ready to debate. I just want that soft set theory and hybrid structures must be developed using correct ideas of Prof. Molodtsov.
Thanks
Santanu Acharjee, PhD
(Collaborator of Prof. D. Molodtsov,
Title of the paper: Soft rational line integrals, published in 2021 and two more in submitted form)
Assistant Professor
Department of Mathematics
Gauhati University, India
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Dear Dr. Fawaz,
Kindly don't share me the chapters with incorrect ideas on soft set theory. Read my questions at first very carefully. Publication of a paper on soft set doesn't mean that the notions, definitions, etc. of soft set used in the paper are correct.
Don't be blind to accept the truth that Prof. Molodtsov raised several questions on this incorrect notions and he published several paper.
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I'm running 100 ns long MD simulations of a small peptide in isolation or bound to a partnering protein. My goal is to produce a plot of the residues in double helical form from start to end along with a video of the structure using Chimera.
The steps I take after a MD run are...
Step 1:
Center the trajectory file:
gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center
--- Type 1 for protein and then on the next prompt 0 for system.
Step 2:
Calculate the back bone rmsd of the entire complex:
gmx rms -s em.tpr -f md_0_1_noPBC.xtc -o rmsd_xtal.xvg -tu ns
--- Type 4 then 4 for backbone RMSD calculations
Step 3:
I then make an index file of the two chains:
gmx make_ndx -f md_0_1.gro -o index.ndx
--- Type "splitch 1" hit enter, type the number of what chain I want to reference (typically "2"), then type "q" to exit
Step 4:
From there I want to produce a trajectory file (.xtc) from the index and an updated topology (.tpr) file from my MD run using the index file:
Step 5:
Trajectory of just chain 2:
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -n index.ndx -o chain2_traj.xtc
--- Type the chain I want to reference (typically "19")
Step 6:
Topology of just chain 2:
gmx convert-tpr -s md_0_1.tpr -n index.ndx -o md_chain2.tpr
--- Type the chain I want to reference (typically "19")
Step 7:
I then center the updated files:
gmx trjconv -s md_chain2.tpr -f chain2_traj.xtc -o chain2_traj_noPBC.xtc -pbc mol -center
--- Type "1" then "0"
Step 8:
I then perform my analysis using dssp and rms
gmx do_dssp -f chain2_traj_noPBC.xtc -s md_chain2.tpr -sc scount_chain2.xvg -o ss_chain2.xpm -dt 10 -sss H
--- Type "5" for mainchain
Step 9:
gmx rms -s md_chain2.tpr -f chain2_traj_noPBC.xtc -o rmsd_xtal_chain2.xvg -tu ns
--- Type "4" then "4" for backbone rmsd
*** The issue I run across is when I open the tpr and xtc files in Chimera with the MD viewer, the peptide is completely wrong. What I've deduced is that the topology (tpr) file for some reason gives each atom in the first few residues their own residue id's. Thus residue 1 actually makes up residues 1-9 (or something similar). However, when I produce a pdb from the trajectory file (.xtc) with:
'''
gmx trjconv -s md_chain2.tpr -f chain2_traj.xtc -dt 100 -o trj.pdb
'''
The peptide is correct. So I believe the issue is that the topology file is being produced improperly due to a bug or something wrong with my steps above. I've also tried using the em.tpr file for input on step 6, but I run across the same issue. This is happening with several different peptides. One peptide that is 65 amino acids long and one that is 18 amino acids long. On the 65mer, it appears to only happen on the first 4-5 residues. ***
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I am starting a new area of research that is Algebraic topology. Kindly suggest some latest problems and related publications
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@peterkepp
I have started reading algebraic topology from three book
Topology by J Munkres
Algebraic Topology by A. Hatcher
Basic of Algebraic topology by A. SHASTRI
But I can confused from where did I find the research problem and the recent papers are too advance for me
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I am trying to generate OPLSA topology for LiTFSA using LigPargen tool. But it is showing an error. Are there any other tools for generating OPLSA topology parameters in Gromacs?
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I want to simulate a grid-road topology (organized streets) with vehicles generate traffic to Road Side Unit (RSUs). Also, if I need to ramp up quickly to 100 or 200 vehicles how can I do that?
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Sai R N Thank you.
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Suppose, If I am doping a topological insulator let's say Bi2Se3 with an external magnetic ion whose spins order in-plane (easy axis in ab plane ), what could be the corresponding changes in the Dirac cone below the ordering temperature?
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As asphalt has various components, how do we create a topology for asphalt.?
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I am doing research on topology optimization, filling a unit lattice with different materials, and I want to use the homogenization theory to calculate the static effective elasticity tensor of the unit cell, as shown in the file .
How to set comsol to calculate E33 in 2D model?
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Usually, systems, where conduction electron acquires a berry phase due to noncoplanar spin structure, are topological hall effects. Is the geometric hall effect another name for the same effect?
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"In crystalline solids, where the wave vector k becomes a good quantum number, the wave function can be viewed as a mapping from the k-space to a manifold in the Hilbert space (or in its projection), and hence the topology becomes relevant to electronic states in solids" - This is a statement in the introduction of Yoichi Ando's comprehensive review on topological insulators. Ref: Ando Y., Topological insulator materials, J. Phys. Soc. Japan, (2013), 82, 102001.
I find it difficult to understand why k being a good quantum number allows for the wavefunction to be viewed as a mapping from k-space to a manifold in Hilbert space. I would appreciate to receive some insights on the statement given in quotes. Other approaches to explaining why Hilbert space topology becomes relevant to electronic states in TI are also welcome. Thanks in advance.
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Well, they lead to the localization of light which are transversal waves and have a sort of elliptical polarization, among many other interesting phenomena, Prof. Stam Nicolis
You can check for example:
Best Regards.
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1. In a TI surface state/edge state, each k state exists in pairs. The Dirac cone in a 3D-TI has a -k state for every +k state.
2. Due to spin-momentum locking caused by high Spin Orbit Coupling (SOC), the -k state will possess opposite spin to that of +k.
Am I correct in understanding that the combination of these two conditions is what makes the system be termed as a time reversal symmetry protected system? That is, k needs a -k (Kramer degeneracy), and the -k state is opposite in spin also. Hence a TR operation completely reverses the state.
If yes, my question is the following:
What physical properties (band structure, crystal structure) of a system causes a material to possess the Kramer degeneracy? That is, physically what causes a material's band structure to possess k states in pairs?
But, the kramer degeneracy theorem is defined as: 'every eigen state in a TIME REVERSAL SYMMETRIC system with half integer spin will have at least one other degenerate eigen state'. This definition makes it seem like TRS is one of the requirements for the kramer degeneracy.
I am confused about which is the cause and which is the effect here? Does TRS cause the Kramer degeneracy? Or is the presence of the Kramer degeneracy along with spin-momentum locking causing the system to be called time reversal symmetry protected?
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A good review to complement the answer by Prof. Stam Nicolis on time reversal symmetry is the classical book by Prof. A. Messiah, the chapter on symmetries and invariance, in the old separate version it was chapter XV, Dr. Abhirami Saminathan
Best Regards.
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Hi everyone, I am doing topology optimization in 3D, and I want to simulate and print the optimization result, but my optimization result has many steps, it is not smooth, so the exported STL file has a lot of meshes, I would like to ask if there is any way to make the topology optimization result smooth?
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You might consider VisPER. All you need is a finite element model and the information about the pseudo-density distribution (void/solid) of your design element.
A free education edition is available at https://www.intes.de/edu
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Does anybody have any idea how to execute an user defined python script in the middle of a mininet wifi script just after the topology is created and then manipulate the nodes based on the results of user-defined python script. Please help. If anybody knows then please send me the steps or an example script.
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with the help of sage you can explore too much.
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A physics experiment [1], driven on an expanding spin-orbit coupled Bose-Einstein condensate, suggested that a self-trapping effect band (explained in terms of the Peierls-Nabarro energy barrier) separates two dispersion domains characterized by a positive mass but a spin reversal. The self-trapping phenomenon was naturally explained by a negative effective mass related to a negative curvature of the underlying dispersion relation (as opposed to parabolic curvatures).
To better contextualise my question from a practical point of view, I will quote Wikipedia ( follow https://en.wikipedia.org/wiki/Spin_(physics) ): “Mathematically, quantum-mechanical spin states are described by ‘vector-like objects’ known as spinors. There are subtle differences between the behavior of spinors and vectors under coordinate rotations. For example, rotating a spin-1/2 particle by 360° does not bring it back to the same quantum state, but to the state with the opposite quantum phase; this is detectable, in principle, with interference experiments. To return the particle to its exact original state, one needs a 720° rotation (The Plate trick and Möbius strip give non-quantum analogies).
I appeal here to physicists in a spirit of free and friendly discussion.
  1. Khamehchi et al., “Negative-Mass Hydrodynamics in a Spin-Orbit–Coupled Bose-Einstein Condensate”, 2017 - https://www.researchgate.net/profile/Thomas-Busch/publication/311612111_Negative-Mass_Hydrodynamics_in_a_Spin-Orbit-Coupled_Bose-Einstein_Condensate/links/5a97b63845851535bcdee6fd/Negative-Mass-Hydrodynamics-in-a-Spin-Orbit-Coupled-Bose-Einstein-Condensate.pdf
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"It was also shown that the left- and right-chirality quaternions can be used to describe Lorentz boosts with constant velocity in an arbitrary direction"
"[...] an interesting connection between the non-commutative split-quaternion division algebras and the uniqueness of our four-dimensional spacetime is pointed out by introducing a super split-quaternion formed of a superposition of either the left- or right-chirality versions of the generalized split-quaternions. It is shown that the norm of this super split-quaternion has a form identical to the distance function of our four-dimensional spacetime. This paves a way to an interpretation of our four-dimensional spacetime and its physical properties based on a superposition principle of fundamental structures of our physical world, which can be represented by division algebras"
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I am screening few drugs against a targeted enzyme using autodock 4.2, i had obtained best conformation now in order to perform MMPBSA, i am working with Gromacs.
The pdb file for the selected cluster was obtained by saving the cluster in .pdbqt format later i had opened the file in pymol and re-saved the file to .pdb....now by following standards tutorial available from the Gromacs tutorial, after seperation of both the pdb, and converting the ligand pdb to .mol2 formate when i used swiss param web site for generating topology file for ligand it was showing error.
So question is should i use the same ligand.mol2 from the autodock generated cluster or can I proceed by re-downloading my ligand file from zinc data base and continue my stimulation or should I should use the ligand coordinates that i got from autodock Vina....."as i am facing trouble to generate the topology from coordinates that i was obtaining from the autodock 4.2 is there any solution to fix it"
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After separating your ligands keep them in a .pdb format and then you can use the PRODRG server to generate a topology without any error
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Hello,
I am currently working on something that requires cycle accurate simulations (TLM) for NoC that contains Irregular Mesh Topology(ies) / completely arbitrary topology(ies).
Also routers should support X no. of ports instead of standard no. of ports.
Could you please name a few free simulators that support the above mentioned features.
Thank you in advance & best regards
Manikanta
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Thank you for trying to answer my question ma'am.
Cisco packet tracer, from my understanding, is a large scale network design/visualization tool.
But, what I am looking for is on chip network simulation tool which is used for an SoC architecture exploration.
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I want to know about introduction, definition, explanation, examples and application of soft multi set topology
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The multi set (mset) topology you asked for is given in the following article:
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Hi ,
I am facing some problems in my ligand-protein (docked complex) simulation.
-------------------------------------------------------
Program: gmx grompp, version 2019.5
Source file: src\gromacs\gmxpreprocess\grompp.cpp (line 610)
Fatal error:
number of coordinates in coordinate file (complex_solv.gro, 61208)
does not match topology (topol.top, 61207)
For more information and tips for troubleshooting, please check the GROMACS
-----------------------------------------------
I already searched on the internet and tried to figure it out by myself but couldn't. I am attaching the topology and gromacs files too.
Please help me figure this out if anyone can. Thanks
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have you used -p topol.top option in your command??
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Hello everyone,
While performing MD simulations of protein - ligand complex, at the adding ions stage I am facing an error :
Fatal error:
Syntax error - File UNK_fix.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
Well, since I've used Swissparam to write the topology file of the ligand (UNK_fix.gro) which usually uses CHARMM all atom forcefield and the protein topology I've written with the charmm36-2019.ff. Can this be a reason that I'm facing the above error?
I've also referred to other options like #include statements which I suppose are correct and the editing in topology is all done right. For reference:
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include ligand topology
#include "UNK_fix.itp"
; Include water topology
#include "./charmm36-mar2019.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "./charmm36-mar2019.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein 1
UNK 1
SOL 24553
So, please guide me through any other suggestions which may correct this error.
Thank you in advance!
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Thanks for your response. Actually, I´m working with SwissParam, as you were at the beginning of your question, but I´ll try ATB if that solves the issue. Thanks!!
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While running the command gmx mdrun -deffnm nvt I was facing an error
Step 0: The total potential energy is 3.94046e+16, which is extremely high.
The LJ and electrostatic contributions to the energy are 3.94046e+16 and
-1.10841e+06, respectively. A very high potential energy can be caused by
overlapping interactions in bonded interactions or very large coordinate
values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology.
how to overcome this please help me out
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Hi Amanpreet Kaur,
Have you initially performed the energy minimization run? It seems several unusual bonds might be present in the simulation system. In order to escape from this artifact use the systematic approach to stabilize the model system.
1. perform energy minimization run
2. applying the position restrained potential perform a short run at 200K using NVT ensemble.
3. NPT run, at desired temperature releasing position restrained potential
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I aws running the command gmx grompp -f ions.mdp -c 1ua7_solv.gro -p topol.top -o ions.tpr -maxwarn 1 but I encountered an error stating number of coordinates in coordinate file (1ua7_solv.gro, 90855) does not match topology (topol.top, 90854). How to overcome this . Please help me out . I am attaching both the files and screenshot of the error.
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Hi,
In you topology, there are two compounds named "UNK" and "UNL", while in the *.gro file, there is only one of them, 'UNK', while there is no 'UNL' in the coordinate file (*.gro). Therefore, either UNL (1mol) is extra in topology or you did not add UNL coordinates in the *.gro file. Once, you address this, I hope the error will go away.
Good luck
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During the topology generation of protein (PDB id: 6lu7), a fatal error occurred. How to resolve this error and what precautions should be taken to avoid such errors?
Thanks in advance.
Regards,
Vinay
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I suspect it has to do with the non-canonical residues in chain C: 02J in position C1 ( 5-methyl-1,2-oxazole-3-carboxylic acid, https://www.rcsb.org/ligand/02J ), PJE in position C5 ( (E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid, https://www.rcsb.org/ligand/PJE ) and 010 in position C6 ( phenylmethanol, https://www.rcsb.org/ligand/010 ). Chain C is a ligand to the protein. If you are interested in just the protein, e.g. in preparation for docking, you should remove chain C. If you actually are interested in the complex, you need to supply the topology and parameter files for these hetero-compounds as you would for non-peptidomimetic ligands.
To avoid such problems, start by looking at the structure in a molecule viewer to look for non-proteinic components ( e.g. PyMOL selection "organic" ) and/or look carefully at the annotations at rcsb.org ( https://www.rcsb.org/structure/6LU7 ), listing Entity ID 2: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
In addition, the biological unit of the protein is a homodimer. However, since the dimer symmetry coincides with crystallographic symmetry, the asymmetric unit only contains one monomer. Depending on the questions you wish to adress with your computational analysis, you might want to use the biological assembly rather than the asymmetric unit of the structure.
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Hi, everyone! I developed a ML tree using IQtree, then I uploaded output file (.treefile) into itol and Figtree. I got different tree topologies using itol and Figtree. Any idea why? If someone could assist me, I would be grateful. Thanks :)
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Follow
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Dear researchers
I try to perform molecular dynamics many times, but I get the following fatal error - UNABLE TO FIND ANGLE PARAMETERS FOR CG2R61 NG2RC0 NG2RC0 (ATOMS 4981 4986 4977). I attach the .pdb-file (for protein-ligand complex) and .str-file with topology of ligand (by CGenFF). Please help me to fix this error.
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Hello Roman! Did you try CharmGUI? Please have a look
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i was running the energy minimization step using the command gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr in gromacs but the error occurred of mismatching of atoms how to correct this? I am attaching both the files of topology and em.gro
thanks
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It means the number of atoms in the topology and coordinate file are not same.
I find there is a blank line at line 18750 (after number of protein and before of number of solute). So, I think the grompp can't read your solute number due to the blank line. It seems the grompp think that the blank line in the number of atoms is EOF (end of file).
Therefore, I think that you just need to remove the blank line and try run grompp again.
Best regards,
BEFORE
-------------------------------
[ molecules ]
; Compound #mols
Protein_chain_A 1
UNL 1
SOL 35130
NA 4
AFTER
______________
[ molecules ]
; Compound #mols
Protein_chain_A 1
UNL 1
SOL 35130
NA 4
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Hi, I tried to do topology optimization on wheels as part of my dissertation trying to make light weight wheels for a student formula car but don't understand what I'm doing wrong. I'm using ansys
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Hallo,
1. Material should be clustered.
2. There MUST BE some boundary condition is wrong, because of the completely disconnected in the central area. In addition, the pressure of the inner tube should also be considered, or just make the contacting area non-designable.
3. Circumferential repetition conditions should be added.
4. Element size is too big, which is a general problem in FSAEers. With such small elements to make topology optimization is serving no useful purpose at all.
I wish you a light and strong job in advance.
Best Regards,
Wei Huanxia
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getting .str file for a given molecule through CGenFF is almost a simple task but how we can further achieve the topology and parameter file for actual tasks.
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  1. conda activate
  2. conda create -n networkx
  3. conda activate networkx
  4. pip install --upgrade pip
  5. sudo pip uninstall networkx
  6. sudo add-apt-repository ppa:deadsnakes/ppa
  7. sudo apt-get update
  8. sudo apt-get install python3.6
  9. pip install networkx==2.3
  10. python3 cgenff_charmm2gmx_py3_nx2.py JZ4 jz4_fix.mol2 jz4_fix.str charmm36-jul2021.ff
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Even after including all the forcefields in the topology file still facing this issue. I am attaching the files supporting. Complex is intact with ligand but while adding ions :
gmx grompp -f ions.mdp -c solv_sp.gro -p topol.top -o ions.tpr
Facing the error
Fatal error: Syntax error - File ffnonbonded.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes?
Please guide with your suggestions
Thank you in advance!
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I would like to suggest you to follow google by typing some related sentences of appropriate words. In particular following some related tutorials via gooling may be more helpful.
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I have prepared a new Cd based MOF. I want to do some topological analysis. Is there any software available? Any help will be greatly appreciated.
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need power set of topology
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Hi everyone,
I work on Abaqus for a project and I want to optmise a part (topoogy + shape). I created the model an ran the topology optimisation. Now I want to extract the result geometry to make some shape optimisation. Is it possible to make it directly from Abaqus or with a Pyhton script or do I need to convert it in a CAD software ?
Thank for your help
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I have created 44 Video Lectures for ABAQUS Python Scripting:
suitable for beginners and experts.
The corresponding Code can be found at github:
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I have a streel structure and the welds need to be merged in share topology in SpaceClaim in order for the elements of both parts to match.
But the contact between beam must no be merged in shared topology so that I can make a contact frictionless in Mechanical.
I can only manage to either separate all bodies so that they all make contacts (but mesh does not match) or merge all bodies so that mesh matches (but no contact surfaces are created and I cannot make the beam-beam contact frictionless).
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I have found a solution for the above said problem. Bodies grouped under a single part in Design modeller can have selective shared topology using the option of 'Connect'. You may refer to this under the section of 'Selective Shared Topology: Using Connect after Share Topology' in Design Modeller User's Guide for further information.
Thanks.
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Fatal error:
Residue 728 named ALA of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
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The naming for the calcium ion in the file is supposed to be CAL, not CA.
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Defining similarity function or relation in Case Based Reasoning is a key moment for a good result. Frequently numeric functions are used, which is, in fact , an assumption of existing some kind of metric, being cases points of the corresponding space.
But what about defining "proximity" of given cases in terms of topological relations? I have being searching but, up to now, I have not found any general approach. Have you any information on this regard?
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Is it advised to use Adaptive-remeshing before topology optimization process? (because sensitive sections on my part (which gain the smallest size of the mesh), are actually frozen in the topology optimization process, and on the other hand, sections that should be removed from topology, have larger mesh and will make coarser surface at the end of the process)
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Cyprien Saito Actually, merely to some extent. My question was that we use Adaptive Remeshing rule to reduce calculations in simulations. In other words, based on some criteria some meshes become smaller and others become larger.
Topology optimization process is a kind of removing excess material from the part to improve its functionality based on another criterion. ( it removes some meshes that are not under stress, loads, etc.) For these reasons, I am not sure whether we can combine these two methods.
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I am aware of the facts that every totally bounded metric space is separable and a metric space is compact iff it is totally bounded and complete but I wanted to know, is every totally bounded metric space is locally compact or not. If not, then give an example of a metric space that is totally bounded but not locally compact.
Follow this question on the given link
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Euh...The closed L^2 unit ball is not totally bounded since it is closed but not compact. The open unit ball is not totally bounded either, since its closure is not compact.
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Ifogsim topology execution
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Dear Haidi Said ,
The ifogsim simulator does not allow you to run a simulation when you create a topology using ifogsim GUI. The GUI is just to draw the topology. You need to create your own topology in the code itself. I guess you are creating topology from src->org.fog.gui.example->FogGui.java right?
Modify the code according to your algorithm.
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Dear Colleagues,
I need some advice to resolve the issues associated with building robust phylogeny trees in different fungal families. It is indeed a basic query but may be helpful to many budding mycologists from India and across the globe.
We are using graphic version of RAxML and MrBayes for making trees.
Unfortunately, we are regularly facing issues related to data deficiency in several fungal families ( It cannot be resolve until sampling and epitypification!!!).
But even after retrieval of data based on some published papers; The BS/BYPP values seem to vary considerably from the high values mentioned in the article to a moderate value in our analyses.
What are the best practices to deal with it?
We choose type strain to build a backbone to assess the topological congruence for different genes too.
How best we must edit our datasets to achieve high BS values? How best we can define gaps in RAxML?
What are the other parameters taken into account other than model tests?
Thanks in advance.
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Yeah, a nice question.
I am a PhD student majoring in Bioinformatics. I have similar problems with Rajeshkumar K. C. . Sometimes even I used same dataset, I couldn't get the similar phylogenetic tree, even with partially incongruent topology.
I think that the difference in alignment tools, tree inferring tools, evolution models, the order of linking multiple markers and trimming methods maybe lead to the incongruence. Specially, I realized that many authors used "manually trimmed" to describe the trimming process, but we do not know what sites were removed. Every one has his own idea in trimming alignments.
In my opinion, no mater what software you use, the author should confirm that, other people can reproduce the phylogenetic analysis based on the original data (sequence accession table) not the alignment files, according to the method description.
In practice, I prefer to use trimal to trim the alignment files, and other people can get identical alignment files according my command options. We can confirm that other people can get most similar or even identical results according to our method description.
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For writing research articles
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read this research paper it will be useful
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I was performing the equilibration and minimization of ATP in namd and vmd.
This is the error message.
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE top_all27_na.rtf
LINE=** \\\\ CHARMM27 All-Hydrogen Nucleic Acid Topology File ////*
Error is showing right in the title line of the topology file. Is there any format issues ?
I have attached the topology file mentioned in the error.
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The best way is to check your equations/functions and then code via step by step execution.
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Hello everybody,
I am new in topology in condensed matter physics. So excuse me if my question were somehow unusual. In Haldane model, we put one step (or steps) forward and take into account the annihilation and creation of the electron in the next-nearest neighbors in writing the Hamiltonian rather than the simple tight binding model, so my question is Why we do not take into account the annihilation and creation of the electron in the third, fourth and ... neighbors? Is this because those sublattices are far away ,so these hoppings are negligible?
Thanks
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Consider the powerful central role of differential equations in physics and applied mathematics.
In the theory of ordinary differential equations and in dynamical systems we generally consider smooth or C^k class solutions. In partial differential equations we consider far more general solutions, involving distributions and Sobolev spaces.
I was wondering, what are the best examples or arguments that show that restriction to the analytic case is insufficient ?
What if we only consider ODEs with analytic coeficients and only consider analytic solutions. And likewise for PDEs. Here by "analytic" I mean real maps which can be extended to holomorphic ones. How would this affect the practical use of differential equations in physics and science in general ? Is there an example of a differential equation arising in physics (excluding quantum theory !) which only has C^k or smooth solutions and no analytic ones ?
It seems we could not even have an analytic version of the theory of distributions as there could be no test functions .There are no non-zero analytic functions with compact support.
Is Newtonian physics analytic ? Is Newton's law of gravitation only the first term in a Laurent expansion ? Can we add terms to obtain a better fit to experimental data without going relativistic ?
Maybe we can consider that the smooth category is used as a convenient approximation to the analytic category. The smooth category allows perfect locality. For instance, we can consider that a gravitational field dies off outside a finite radius.
Cosmologists usually consider space-time to be a manifold (although with possible "singularities"). Why a manifold rather than the adequate smooth analogue of an analytic space ?
Space = regular points, Matter and Energy = singular points ?
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For a function describing some physical property, when complex arguments and complex results are physically meaningful, then often the physics requires the function to be analytic. But if the only physically valid arguments and results are real values, then the physics only requires (infinitely) smooth functions.
For example, exp(-1/z^2) is not analytic at z=0, but exp(-1/x^2) is infinitely smooth everywhere on the real line (and so may be valid physically).
One place where this happens is in using centre manifolds to rigorously construct low-D model of high-D dynamical systems. One may start with an analytic high-D system (e.g., dx/dt=-xy, dy/dt=-y+x^2) and find that the (slow) centre manifold typically is only locally infinitely smooth described by the divergent series (e.g., y=x^2+2x^4+12x^4+112x^6+1360x^8+... from section 4.5.2 in http://bookstore.siam.org/mm20/). Other examples show a low-D centre manifold model is often only finitely smooth in some finite domain, again despite the analyticity of the original system.
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I know nothing about this two related subjects and I need, for the moment, a concise introduction and, later, a more deep explanation with implementation techniques.
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This paper provides a very good overview:
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Hello,
I'm currently working on G6PD mutations and thus want to do molecular dynamic simulations for G6PD protein with its ligands: G6P and two NADP. However, I'm unable to create ligand topology files for the NADP ligand. I have tried ATB server, Lipargen server and swiss param. It would be helpful if anyone could help me with this.
The LigParGen server is giving me the error as follow:
"Sorry, an error has been detected in your input data (file, smile or selected charge):
Found residue ligand NAP
Unknown error. Please, check the input file. If you are not able to find the error, we suggests to use the SMILE code."
The file I used is from molecular docking of ligands to the G6PD protein I modelled, I extracted ligands from PDB (2BH9). I added Hydrogens to the PDB file using Avogadro.
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Yes, the structure, as it is, correspond to a -1 charge. To get a neutral one you should add another H atom on oxygen #10 (or #19).
Best,
Felippe
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Dear all,
I am simulating a peptide with a few unnatural amino acids in Gromacs. I used Topolbuild to get topology files for the peptide. I cannot get dihedral angle parameters when I use recommended setting.
May I know, why should I not get such parameters using recommended setting?
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We usually use Strain Energy as an objective with volume constraint in topology tasks. But if I want to reduce the mass/volume reduction of structure as much as possible until displacement along the 3 -direction is equal to -1.
Did anyone know, how to do that?
When I choose the (Displacement, 3-direction) minimum value in the design response, I get this error "The minimum operation cannot used be with the given identifier"
How to deal with this?
Thank you a lot!
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Can you share your Abaqus model (.inp)?
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Hello everyone, I am trying to simulate the protein-ligand complex with Zn ion but during solvation i am getting the following error:
Fatal error:
Syntax error - File LIG.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
I tried many ways but not able to solve this issue
My topology file
Topology file:
; Include forcefield parameters
#include "amber03.ff/forcefield.itp"
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Ion_chain_A2.itp"
; Include ligand topology
#include "LIG.itp"
; Include water topology
#include "amber03.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "amber03.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Ion_chain_A2 1
LIG 1
SOL 27420
I also placed ligand itp file below forcefield parameters but it doesn't work. If you guys have any idea how to tackle this problem please help me. Thank you.
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Hello,
I checked the topol.top where the forcefield parameters lines in top while in older version the force field parameters defines in last section of topol.top
so you have to define your ligand .itp in below forcefield parameters lines.
ex.
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2020.4 (-:
;
; Executable: /apps/GROMACS/2020.4/bin/gmx_mpi
; Data prefix: /apps/GROMACS/2020.4
; Working dir:
; Command line:
; gmx_mpi pdb2gmx -f protein.pdb -o complex.gro -ignh
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters
#include "charmm36-feb2021.ff/forcefield.itp"
#include "AW_GMX.itp"
.....
[ molecules ]
; Compound #mols
Protein_chain_A 1
LIG 1
SOL 13404
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I started to add recently the gap partition in my ML analysis of ribosomal genes because it improves the results. To perform my analysis I use the online version of RAXML at Cipres Gateway. I add the gap partition as binary data [1/0] with ascertainment_correction_lewis.
However in my last analysis, where few short sequences were present together with other longer, I obtained an unexpected result. The short sequences clustered together, even if not related, in the wrong position and they were showing very long branches. An other short sequence was in the correct position but also showed a very long branch. The latter sequence covered the ssu-its part, where most of the gaps where present, while the formers covered part of the lsu.
I deduced that the abnormal topology of the tree depended on the missing data in the gap partition, codified by '0' like the absence of gap. In other words the short sequences [not covering the its] had a big part of gap partition identical because of a long list of '0'.
There is a way to overcome this problem without trigging the sequences at the same lenght?
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Hi Alison, thank you for your answer. Actually I solved my problem long time ago. My issue was that gaps, when absent, were coded in the same way (=0) of missing data. Now I have changed the program to codify the gaps in binary data and I use 0 for gap absent and - for missing data.
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Dear all,
The reason I am trying to simulate the sheet, I want to add the graphene sheet as a substrate in a cubic box and evaporate some molecules on it. Unfortunately, I had a problem while trying to  run energy minimization using  (gmx grompp -f minim.mdp -c GRM_w.gro -p grm_w.top -o min1.tpr) I got the below error: Fatal error: number of coordinates in coordinate file (GRM_w.gro, 146535)              does not match topology (grm_w.top, 156815).
some differences between my simulation and the one in the website:
1. I am using gromos54a7 instead of charmm36. The reason for using gromos 54a7 that I will need to evaporate some molecules on the graphene sheet and they should be evaporated using gromos 54a7.
2. I am using GRM instead of GRA.The reason for using the GRM is that I found the graphene sheet.itp online for the gromos 54a7 and it was named GRM and hence, I had to name everything GRM to match the names in the .itp that I included.
The steps I did using the terminal on Linux :
1. cd and go to directory
2. create a text file named GRM.gro and paste the data belwo in the file:
GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring
4
1GRM C1 1 0.061 0.071 0.000
1GRM C2 2 0.184 0.142 0.000
1GRM C3 3 0.184 0.284 0.000
1GRM C4 4 0.061 0.355 0.000
0.245951 0.426000 0.284000
3. gmx genconf -f GRM.gro -o GRM_sheet.gro -nbox 15 10 1
create the graphene sheet
4. I created the file graphene.n2t and attached the below
C CG2R61 0.00 12.011 1 C 0.142 C CG2R61 0.00 12.011 2 C 0.142 C 0.142 C CG2R61 0.00 12.011 3 C 0.142 C 0.142 C 0.142
5. I created a new file named grm_w.top and included the forcefield, the water model spc and the graphene sheet.itp that I found it online.
; Include forcefield parameters
#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/forcefield.itp"
; Include topology for GRA
#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/GRM4x.itp"
; Include water topology
#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/spc.itp"
[ system ]
; Name
GRM in water
[ molecules ]
; Compound #mols
GRM 1
SOL 50
6. I chanegd the size of the sheet in the z direction using:
gmx editconf -f GRM_sheet.gro -o GRM_sheet_new.gro -box 10 15 10
7. I solvate the system using:
gmx solvate -cp GRM_sheet_new.gro -o GRM_w.gro -p grm_w.top
now the topology file grm_w.top was updated and a line was added as below:
; Include forcefield parameters
#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/forcefield.itp"
; Include topology for GRA
#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/GRM4x.itp"
; Include water topology
#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/spc.itp"
[ system ]
; Name
GRM in water
[ molecules ]
; Compound #mols
GRM 1
SOL 50
SOL 48595
now I have 2 SOL which I don’t know what should I do.
8. I included in my minim.mdp file a line with : Periodic_molecules = yes
9. I tried to run energy minimization using:
gmx grompp -f minim.mdp -c GRM_w.gro -p grm_w.top -o min1.tpr
and I got an error:
Fatal error:
number of coordinates in coordinate file (GRM_w.gro, 146535)
does not match topology (grm_w.top, 156815)
END of steps.
I read that if the difference between the 2 numbers is devisable by 3, it means that the problem in the solvate and you can change the number manually to match the other one. But it is not the case here. I also thought that the problem might be that I have 2 SOL lines in the .top and I removed the SOL 50 line but the difference decreased by 149 only.
Looking forward for your help, I have been trying for many days without success.
Attached are all the files I used it including steps file which contains all the steps I did as written above.
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Hi, saw this question pretty late. My suggestion would be to delete the initial line SOL 50. Now, either use a script, or simply a vmd to check the number of water molecules. Then finally update the number of water molecules. It should work fine now.
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This paper is a project to build a new function. I will propose a form of this function and I let people help me to develop the idea of this project, and in the same time we will try to applied this function in other sciences as quantum mechanics, probability, electronics …
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Are you sure you have defined your function correctly?
1. Usually z=x+iy. But in your function z is in the limit, thus being in both the arguments and what the integral is computed against. If z is not x+iy, the function is not a function of (x,y).
2. What do you mean by limit? Do you want to compute the case when z->0?
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In the article "On the topology of a free locally convex space" by V. V. Uspenskii the exchange between an inverse limit and (which in my opinion is) a left adjoint functor is used. Specifically, if X is the inverse limit of an inverse system {X_\alpha : \alpha in A}, and F is a left adjoint functor, in which cases we have that F(\lim X_\alpha)=\lim F(X_\alpha).
I know that the exchange occurs when we are taking direct limits (topological sums for example).
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Sorry if I don't use the conventional names, colimits are direct limits, and limits are inverse limits. I also recognized the statements of your answer, it is indeed true that:
Left adjoints preserve colimits
Right adjoint preserve limits However, and reframing my question, is what Uspenskii does in the afore mentioned article valid?
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We are working on the linear topology of multiple APs, but the connection between stations in different APs cannot be verified unless we add an SDN controller to the network! Is there any method to make this connection possible? because we want to compare the network in two cases: with and without a controller.
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If I wanted to link algebra and topology in order to specialize in algebraic topology (mathematics), what researches would you recommend me to start reading with?
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Hamed Sadaghian Thank you, this is very useful for me.
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Hi all,
I want to predict the sorbed amount of 0.5 M sodium sulfate solution with my ferrihydrite powder. The measured specific surface area is 190 m2/g. I also found the topological polar surface area of sulfate ions to be 88.6 A^2. I am trying to using the following number to calculate for the sorbed volume (Vm): S = [Vm*Na]/[mx22400], where N = Avogadro constant; m = mass of sorbent; a = cross sectional area of sorbate.
However, I got a ridiculous result, so I am not sure which step did i do wrong? Or I should use another equation to solve this problem.
Any input/suggestions are highly appreciated!
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Hello, did you check all the units in your calculation. The value 22400 is related to the volume of one Mole of air in standard conditions?
Gabriel
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Here we discuss about one of the famous unsolved problems in mathematics, the Riemann hypothesis. We construct a vision from a student about this hypothesis, we ask a questions maybe it will give a help for researchers and scientist.
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I put together a solution of the RH myself. While it can't be considered a complete proof while not vetted by experts, it presents various strong arguments and a real breakthrough, which is the inversion formula for Dirichlet series. Given any Dirichlet F(s), you know a(n) from F(s). Unfortunately, it's impossible to have an integral representation for a(n) usually, it's a Taylor power series. Please head to my page for the paper.
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Hello,
I am trying to run the IMa3 software on my data set. I have a SNP data set. I have a feeling that the input format requires sequence data to infer the topology. Is there anyone who can help me understand what the input data would look like?
Thanks
Giulia
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Hey Giulia!
You're entirely correct. PGD has trouble when making an Ima file directly.
On PGDSpider, get a phylip file from your .vcf first. It will have a .txt extension; leave it like that. Then use that .txt as input to make the Ima file, also on PGDSpider. I tried it by myself, and it worked.
Cheers!
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I am getting immersed in The Kervaire-Milnor Formula, where each term of which connects with a different field in mathematics: "The number of differential structures on the 4k − 1-dimensional sphere is given by a quantity that is the product of three quantities: Elementary factor × “Non − J Classes” × Numerator of B2k/2k". Information read in https://people.math.harvard.edu/~mazur/papers/slides.Bartlett.pdf
My research is focused on how to connect the Turán moments and coefficients of Jensen polynomials for the entire function Xi as I have noticed some valuable results. I would like to count with more articles or information about the Bernoulli numbers visible in topics of topology which could involve the Turán moments and Jensen coefficients as well.
Thanks in advance!
Carlos
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Is B2K a bug of the millennium sort of thing? is that what you're asking?
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Program: gmx mdrun, version 2019.1
Source file: src/gromacs/mdlib/sim_util.cpp (line 752)
MPI rank: 3 (out of 4)
Fatal error:
Step 700: The total potential energy is nan, which is not finite. The LJ and
electrostatic contributions to the energy are 0 and 0, respectively. A
non-finite potential energy can be caused by overlapping interactions in
bonded interactions or very large or Nan coordinate values. Usually this is
caused by a badly- or non-equilibrated initial configuration, incorrect
interactions or parameters in the topology.
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Hello Susheel,
Thank you for your suggestion.
I ran 1 microsecond NPT equilibration for coarse grained system, after that i ran production run, but i am still getting same error in production run.
Please suggest me how do you ran longer equilibration step if it is showing error (The total potential energy is nan, which is not finite)?
I am running by using -append option but after 5ns or 10 ns run it show same error, in this way i completed 1 microsec NPT equilibration.
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Dear all,
I converted a PDB file into Mol2 file using Openbabel (H added) and then fixed the bond order number using this command: perl sort_mol2_bonds.pl jz4.mol2 jz4_fix.mol2
When I try to generate the topology file for my ligand molecule using CGenFF server I get the following error message:
"readmol2 warning: atom or bond number too high; skipped molecule..." (Screenshot attached)
I get a different error on SWISSSPARAM for same file as following:
"Failure report: It was necessary to change the name of the atoms numbered" (Screenshot attached)
Could you please shed some light on what exactly could be wrong here to fix the problem?
With this topology file, I wanted to run an MD simulation of the Protein+ligand complex.
Many thanks,
Deepak
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have you found any solution to this . i am facing the same issues with my mol2 file
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I have a problem with ligand-protein simulation in Gromacs. For research I need an MD simulation of the low molecular weight ligand and colchicine site of the tubulin dimer. Following Justin A. Lemkul's tutorial, I created a separate ligand topology file (using CGenFF) and a protein topology file. Probably because of the simulation of two protein alpha and beta chains, my protein topology file (topol .top) is different from the example topology file in Justin A. Lemkul's tutorial. Regardless of where in the topol. top where I write the parameters of the ligand topology, after creating the box and its solvation, the ligand is not rendered using PyMol. Also, the ligand topology data are absent in the solv.gro file after the complex solvation procedure. What am I doing wrong? Help me please
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complex.gro, line 2: 13308 atoms, UNK atoms not counted.
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Hello! For our research we need to do simulations of GPI-anchored proteins in membrane with Martini force field. But we don't understand how to generate topology for protein with covalent modifications in Martini. Can you help? We are working with three-finger neuromodulators (Lynx1, Lynx2, Lypd6, Lypd6b). Thanks in advance!
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I am currently doing a topology optimization of a given elastic tensor. My cost function is the square of the difference between the target elastic tensor and the elastic tensor, and my volume constraint is in the form of an equation, but I don’t know how to modify the MMA The parameters in make it applicable to least square optimization. I have read the notes of Professor Krister Svanberg and tried some, but still no success. Has anyone done similar optimizations? Can you give me a little help? Thank you everyone.
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You may focus on topological manifolds optimization. Very beautiful work on this area is here : https://www.manopt.org/downloads.html
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A combined topology of two converters with common elements is to be designed, where switching between the two converters can be done only when required (no importance of frequency of switching here). After switching ON/OFF each of the converters will be controlled differently and they will be completely independent.
So if contactors are used, conduction losses would be higher. Even if semiconductor switches are used then we need a bidirectional and bipolar arrangement of switches, the number of switches will increase and the conduction loss in them will also be present.
So I want to know what can be the other methods for this one-time switching because I want the path to be like the simple conductor with minimum or no additional losses. Or what kind of switching would be best here?
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Isn’t there resonance amongst fresuencies of « common elements » and of « converters setting » ?
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Just as what I have asked, did anyone have done some research about this? I am so interest in it but I have no resource to do this, hoping someone had done and willing to share the result.
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Dear Yunguang,
It is always the case that research in model organisms needs to be extended to other organisms of more interest in specific disciplines - so good luck in finding out more!
Andrew
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Protein-Ligand Complex was generated after performing site-specific docking in AutoDock 4.2.
I am following the MD-Tutorials by Justin Lemkul.
Often bulky antibiotics are administered for therapeutic purposes. For building topologies for protein and ligands, both are separated using the 'grep' command.
When the ligands are visualised in Avogadro, sometimes the ligands seem broken or distorted thereby unfit for topology building.
I'm Using GROMACS 2020.1, CHARMM force field (Feb 2021), CGenFF server for building ligand topology.
Kindly provide some suggestions to resolve the issue.
Thanking you in advance
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With the grep command you are separating the coordinates of the atoms from a pdbqt format without taking into account the unions. I recommend that you isolate separate the model of interest from your pdbqt and use openbabel to generate any other format.
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I need to create coarse grain (CG) beads from all-atom, for which I need to generate the psf file. To create the psf file VMD requires the topology file. So how can I create the topology file or Is there any other way that I can use to construct CG beads out of my all-atom i/p.
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Dear all,
After running the topology validation for the landuse dataset of a single district (polygon), I found over 2000 topology errors "must not overlap" in the data. I am wondering if there is possibility to automate the error fixing procedure with ArcPy. Because at the end of the day, I have to process landuse data for 20 districts at minimum. Thus, it might take months by using error inspector and manualy fix one-by-one. Thank you very much for any help & suggestion.
Kind regards,
Triet
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How to use gromacs to build topology after peptide C-terminal amidation ?
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Dear Dr
you may get some thing here...