General Topology - Science topic

Recently, somewhere on the Internet, I have found the following sentences of H. Brandsma (2018) on semi-open sets:

"No books that I have cover semi-open sets. It is really a marginal subject,

that few people wok in . It is a dead topic of general topology that basically nobody cares about. It is just a way to produce "paper" of little depth or interest."

The "few" and "nobody" are definitely not true. The "depth" and "interest" are certainly also not true. (The characterization of such sets was not an easy game. ) While, the remaining parts may, to some extent, be true.

Dear all ,

I want to simulate a random mixture of POPC lipids and a new molecule (lipid anchor). CHARMM-GUI was used to generate the topology file (.itp) file for the lipid anchor. It also contains another .itp file (charmm36.itp) that has new bonded and none bonded parameters for the new molecule.

When I run grompp command following error was generated. May anyone help me to resolve the problem ?

Thank you in advance !

Hi, i am trying to generate topology files for myricetin molecule for gromacs simulation. The binding partner for it is an unknown protein. I would like to generate the topology files using PRODG server. But the generated files are showing error in gromacs. What are the other ways to generate topology files using other servers?

For MD simulation of protein-ligand, it is important to generate topology file of ligand.

Can someone please help me with a protocol for parameterizing a metallo-protein for MD simulation with amber forcefield? My protein has two FE molecules and the I tried using either frcmod.ionsjc_tip3p or frcmod.ions234lm_126_spce to generate topology but the system is not minimizing. I confirmed that there are no atomic clashes in my system, so I guess the problem has to do with the ions parameters.

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?

I am going to run a molecular dynamics simulation as a part of my research for a protein-ligand complex (NRAS-GTP) using Gromacs. But it has Mg as a cofactor. In literature, I have come across ways to generate topology for protein and ligand. But there is any specific mentioning about Mg ( even though Mg is.a part of the complex). I need to know which is best to be used to generate force field parameters for Mg.

I would be pleased if anyone experienced in this could help me to get through this. Thank you.

Uses in applied mathematics and computer sciences

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!

In general in mathematics we work with groups that includ numbers, generally we work with constants.

So for exempel: For any x from R we can choose any element from R we will find it a constant, the same thing for any complex number, for any z from C we will find it a constant.

My question say: Can we find a group or groups that includ variabels not constants for exemple, we named G a group for any x from G we will find an x' it's not a constant it's another variabel ?

and if it exisit can you give me exempels ?

Hi,

I would like to generate topologies for a couple of small ligand molecules. I have used the Ligand Reader & Modeler of CHARMM-GUI to do that. But the penalty obtained is too much, for example, "param penalty=  25.000 ; charge penalty=  45.141" for a protonated dopamine.

I assume this is caused by inaccurate atom charges? So is it correct to directly replace them with (restrained electrostatic potential charges) RESP or RESP2 charges? Would it make the simulation results more accurate? Also should I change other parameters in the topologies accordingly? Super thanks!

ref: Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)

Hi,

For quite a long time I've been trying to simulate polyphosphate ester molecules using GROMACS software with topology generated with Acpype, but with little success.

The first approach resulted in an error from Acpype:

ERROR: more than one residue detected '{'MOL', 'UNL'}'

ERROR: verify your input file 'mol_att.mol2'. Aborting ...

The input file for this attempt is attached to the post and named "mol_att.mol2". It is puzzling, since there is no MOL named residue. After some investigation the @<TRIPOS>UNITY_ATOM_ATTR section was an issue, it is wrongly interpreted and converted into dummy atoms of newly created MOL residue. In next attempts

I tried to delete invalid fragment and run Acpype again, input file: “mol_noatt.mol2”. It gave me generated topology, but after minimization using parameters from em.gro the output was a distorted molecule.

Is the problem with absence of the attributes section or there is another issue in my molecule that I did not spot?

Best regards.

Hi all,

I am trying to generate the topology of a small organic molecule using the CGENFF server. I have obtained the str file and also have the mol2 file. However, when I run the python code cgenff_charmm2gmx_py2.py to generate the GROMACS files I get the following error.

File "cgenff_charmm2gmx_py2.py", line 1030, in <module>

params = parse_charmm_parameters(prmlines)

File "cgenff_charmm2gmx_py2.py", line 366, in parse_charmm_parameters

ai, aj, kij, rij = s[0],s[1],float(s[2]),float(s[3])

IndexError: list index out of range

It would really be kind of you to provide some help in this regard

Dear colleagues. The text of the question is available in the attached image or pdf-file.

Sincerely, Yaroslav Grushka.

who's registered

as an endorser for the math.GN (General Topology) subject class of

arXiv.

Hi. I want to do simulate via gromacs for ligand- protein complex which there is 9 ligands (three of them are seperated and six of them are connected together(picture in Add files).

when I used prodrg like gromacs tutorial (GROMACS version in the 4.5.x or 4.6.x series.)

itp file for my ligands just had 35 atoms with polar and aromatic hydrogens but in the original pdb file of ligands that I grep from protein pdb (1gyc)there are 126 atomes without hydrogens), so I doubt in accuracy this method for many ligands.

and also I tried to get an itp file from ATB , an error recorded (Found infinite path length because the graph is not connected. Only single, complete molecules can be processed.)

furthermore I tried to use CGenFF, but in step of adding ion i encountered many errors like this

ERROR 1 [file nag.prm, line 31]:

Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported.

all of the 5 ERRORS were similar for ligang.prm file.

can any one guide me how I troubleshoot this problem.?

Hi Dear researchers

i wanna perform a MD simulation of silver nano-particles and some small ligands via gromacs. but i don't know the details of the bonds between Ag atoms and please recommend me how to automatically generate topology file for MD and how to get sample files from topology? (which way is better to this project.)

i get LJ parameter for Ag from liteture

a image of the box has been attached

I have met two kinds of generalized topology: the one defined by A. Csaszar and the one defined by H. Delfs and M. Knebusch. But maybe there are other kinds of generalized topology?

A. Csaszar, Generalized topology, generalized continuity, Acta Mathematica Hungarica 96 (2002), 351-357.

H. Delfs, M. Knebusch, Locally Semialgebraic Spaces, Lecture Notes in Mathematics 1173, Springer 1985.

I am interested in MD simulation of protein molecule in addition with small organic molecules by using gromacs software package. As far I know PRODRG and ATB servers can generate the topology files of small organic molecules but it needs a validation through octanol-water partition coefficient (log P) determination. I have seen this in many papers including Lemkul & Bevan, 2010. So I am looking for a tutorial by which I can do this work easily.

Dear all,

I generated topology of a ligand (ATP) using Acpype which gave me the topology file topol.top and conf3_GMX.itp. I'm writing a report and confused as to what I should write in the report, "I'm using GAFF force field for ATP" or "OPLS/AA force field for ATP". The top line of the topol.top file says #include "oplsaa.ff/forcefield.itp" which caused the confusion. Although the conf3_GMX.itp file seems to have everything and I don't think Gromacs is taking any parameters from "oplsaa.ff/forcefield.itp" file but still I want to be sure. I have attached the topol.top and conf3_GMX.itp file.

My system has only ligand (ATP) and water.

Thanks and Regards,

Raghav

I am working on a protein which has bridging histidine ligand that means it should not have protons at delta and epsilon positions. So while generating topology I want both the nitrogens to be deprotonated but I have options to either have H on epsilon N or on delta N. How to get the desired ionization state? I am using opls force field.

Digital topology, space set topology

Dear all,

I want to generate the topology for ATP(Mg2+) complex using OPLS-AA force field. For only ATP i used Acpype and it worked but when I used ATP(Mg2+) acpype is not working, that's because antechamber use GAFF force field and it doesn't have Mg parameters.

Is there a way I can generate the topology with acpype for ATP(Mg2+)? or Is there any server that can give me the topology that i can use in Gromacs simulation?

Regards,

Raghav

See the attached PDF file for a readable text.

Conjecture $a\setminus^{\ast} b = a\#b$ for arbitrary filters $a$ and $b$ on a powerset cannot be proved in ZF (without axiom of choice).

Filters are ordered reverse to set theoretic inclusion.

$a\setminus^{\ast} b = \bigwedge \{z \in \mathfrak{F} \mid a \leq b \vee z\}$,

$a\#b = \bigvee \{z \in \mathfrak{F} \mid z \leq a \text{ and } z \wedge b = \bot\}$ where $(\mathfrak{F}, \vee, \wedge)$ is a lattice of filters on a fixed set (including the improper filter $\bot$). Note that in my book I use a different notation.

The proof of this assuming choice is available in my online book: http://www.mathematics21.org/binaries/volume-1.pdf

Dear all,

In gromacs tutorial its written that pdb2gmx can be used for cofactors like NAD(H) and ATP, my question is how can i use it on my pdb file of ATP molecule. Do i need to change the residue name? Right now I'm getting the error of unknown residue type LIG.

I want to generate topology files for MD simulations using gromacs.

I have attached my ATP pdb file. Looking forward for a reply.

Thanks and Regards,

Raghav

or please describe some method to generate topology file for a unique structure, such as topology file that exist in tutorial (zero.top).

meanwhile, is there a way to generate top.file for a unique structure from <top_all22_prot.inp>?

I want to do GROMACS simulation using ffamber_99sb forcefield. so that i have to generate the topology of the small molecules by ACPYPE. So can you tell me how to install ACPYPE and Anteamber installation together? Thanks in Advance.

The well-known Zermelio's theorem states that every set can be well-ordered. Since arbitrary well-ordering is a linear ordering, from this theorem it follows the following corollary:

(A) An arbitrary set can be linearly ordered.

It is well-known that Zermelio's theorem is equivalent to the axiom of choice.

Question: Can Corollary (A) be proven without axiom of choice?

I am trying to compute eutectic solvent. ERROR 1 [file darginine.itp, line 65]: Atomtype HS14 not found

I have tried using packmol to set up an initial config and tLEaP to generate topology and coordinates files, but this leads to lots of errors. Does anyone have any pointers?

Please I would like your help on getting an e-copy of the book entitled "The theory of fixed point classes" by Tsai-Han Kiang.

Best regards,

M.S. Abdullahi

I have Designed a Ligand candidate which has an organic scaffold and a small peptide chain with 40 Amino Acid residues attached to it through an amide bond. and I want to set up a MD simulation foe this complex. It was unable to create the topology files for this complex. because it was confusing how to create parameters for the amide bond created between peptide and organic structure.

can somebody please advice me on creating the topology file for this complex to start up the MD simulations

I have the pdb file for my system and have generated the topology files. Now, please help me what i should do to solvate the starch with water. What all should be temp. and pressure parameters? what should be simulation steps?

i am doing simulations in gromacs.

I've tried to follow along Justin's Lysozyme tutorial with Gromacs 5 and noticed that the generated topology has a non-integer charge (qtot 7.887).I have tried to remove the HIS atom responsible for this but still their is a problem in formation of NPT.gro file.

Hi, other molecules is basic but B elemement is not in gaff.dat and I can't use ante-chamber. So How can I generate topology for an element not including in gaff??

The question details are contained in the attached pdf file.

We are trying to generate a nanocluster-peptide conjugate system's topology in ATB for running simulation in GROMACS. The problem is, even if we are submitting the pdb file, it gives an error saying "Invalid structure file". The nanocluster contains ZnO nanocluster wurtzoid structure.

Can anyone shed any light on how to generate the topology?

I am trying to perform a simulation of polymer brushes based on PNIPAM with GROMACS code. 

Generating a coordinate file for the system of interest is not problematic, but creating a topology of this non-linear case is complicated (default gromacs tools are dedicated to linear systems like peptide).

Could you recommend the best tool for this problem (topology generation)?

I am doing simulations on polyethylene oxide and using Trappe force field. Now have got pdb file from materials studio and topology from PRODRG server. But I am facing the problem in dihedral angles in topology file. Please suggest me the solution for this.

I am using Proper dihedral (function:1 ) but the error i am geeting is : Incorrect number of parameters - found 8, expected 3 or 6 for Proper Dih. How to rectify it?

Hi, I am trying to do polymer simulation with gromacs. I am new to

gromacs and trying to construct topology for a system of polymer

chains (POLYETHYLENE OXIDE) using trappe force feild.  My problem is that i am facing difficulties to create pdb file for polymer chain. Is there any server or tool for generating Pdb file other than prodrg server.? 

Dear All,

I have tried to build topology file for a structure that has covalent bond (Between ligand and protein) by using pdb2gmx with the following command:

Where I have tried with three following force fields and water model

But i get the following error:

From the error, I have understood that the reason for error is presence of non standard residue in structure coordinate file.

So, I have generated topology file for BGC(D-Glucose) through prodrug and replace the existing HETATM coordinates by the same but the final minimized structure doesn't even have ligand. (I am not sure this is correct way)

So, If someone knows how to create topology file for structure that has covalent link between residue and ligand.

Thanking you in advance

logical systems associated with topology are some modal lgical system which is compete, now if we exclue the condiation that intersection of two open set ,may not be copen, then will the logiassociated lmodal logical system complete?

in general topology a singleton set can be represented by {x}. how can one represent a singleton set in soft topological space (X,t,E)

general topology implies soft topology but not in converse.Then there should be some topological properties exist in soft topology which is not exist in general topology. do anybody know such properties?

In general topology we have cardinal functions like density, extend, Lindelof number etc. Now the question is how to define similar thing in fuzzy topology also.

Bounded sets are defined on general topological vector spaces, topological modules, topological rings and topological groups. But, I could not find a suitable definition of a bounded set in a topological field.

Any nice material regarding the question will be appreciated.

Am more interested in answers relating to general topology.

By reading the .stl files we can get the geometrical information from the triangular mesh, but can we generate the topological information from the .stl files (in matlab) ??  Is it necessary to define the data structure to generate the connectivity information?? 

I want to create a binary aqueous mixture with DMSO using opls forcefield Since a simple pdb file for DMSO coordinates won't work by input into pdb2gmx, topology files have to be created. What are the steps to be followed for creation of .itp files for DMSO? If I use software like TopolGen or mktop, what changes do I have to make in the files generated? From where do I fill out certain missing information?

Is there any topological space which are not singletons e-closed?

As like compactifications of generalized (or classical) space can we define Lindelofization of generalized (or classical) topological spaces?

here Cp-pointwise topology, C(X) topological ring with usual operations and supremum norm

I have just discovered that a Haudorff compactification of a discrete space can fail to be completely regular in a model for ZF. A helpful paper for it is "Continuing horrors of topology without choice" by Good and Tree (Topol. Appl. 63(1995)); however, I have not seen any papers in which the discovery on compactifications mentioned above is included. I would be grateful if you could tell me whether my discovery is new for all concerned. 

With kind regards. Eliza Wajch

We have already had the reflexive closure (and the transitive closure, the symmetric closure, the reflexive and transitive closure, etc.) of a relation. But how to formally define the Euclidean closure of a relation?

A polyhedron mesh consists convex polyhedrons. Is this formula right: F+1=E+K, F=number of the interior faces, E=number of the interior edges, K=number of the polyhedrons in the mesh? If yes answer, references?

Many thanks.

I want to run an MD simulation for Protein-ligand complex and following Gromacs tutorial of Justin Lemkul Department of Biochemistry, Virginia Tech. I have successfully simulation until the and of the steps. in this case i try to do the similarity simulation with more complex structure that consist of Protein-DNA-and ligan. overall i succesfully generate the topology until em (minimization energy) steps, the graph intepretation looking good,

when write this command i,e mdrun -deffnm nvt some problems were happen following this warning below:

WARNING: Listed nonbonded interaction between particles 3921 and 3945

at distance 3.222 which is larger than the table limit 2.433 nm.

This is likely either a 1,4 interaction, or a listed interaction inside

a smaller molecule you are decoupling during a free energy calculation.

Since interactions at distances beyond the table cannot be computed,

they are skipped until they are inside the table limit again. You will

only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is

probably something wrong with your system. Only change the table-extension

distance in the mdp file if you are really sure that is the reason.

Segmentation fault (core dumped)

what the solution for this problem? thank you

how can i prove the following statement? In other words, how can i prove existence of the following norm?

Let K be any totally disconnected local field. Then there is an integer q=p^r, where p is a fixed prime element of K and r is a positive integer, and a norm ∣⋅∣ on K such that for all x∈K we have ∣x∣≥0 and for each x∈K other than 0, we get ∣x∣=q^k for some integer k.

I want to generate topology file for protein ligand complex to be used with Gromos96 force field. I want a reliable software or website (Except PRODRG 2.5) that can help me achieve the solution.

Generalized topology, Compactifications

i am trying to write a new open (may be which weak /strong)sets.may i know how many open sets (like alpha,beta,gamma, weak,pre etc) available in general topology. can anyone tell me list of open sets.

I want to know relation of these operators  whether these are equal or subsets

I've stumbled onto this property, which applies to a connected topological space: every connected subset has a cut point. I'm sure this has been noticed before. Can anyone shed some light?

I could not find definition of a bounded set in a general topological group in any book. Any help will be appreciated.

Dear Researchers,

I have generated mol2 files which can generate topology and coordinate files successfully using leap package. Can any one guide me if I can generate psf files using VMD ? If so then how I can and what files are required to do so ?

thanks

Hi,

I want to simulate a beta peptide flanked by chemical moieties. I have seen some articles on beta peptide simulations. Most of them have used GROMOS53A6 or 54A7 ff. So, how to generate topology information for beta peptides? Thank you 

It is well known that a bitopological space (BS) is an ordered triple (X,u,v), where X is a base set, and u and v are different topologies on X. A subset G of a BS (X,u,v) is called (u,v)-clopen if G is both u-open and v-closed.

If we change in the definition of compact topological space the words "open cover"--->by "(u,v)-clopen cover " we get naturally notion of (u,v)-clopen compact BS. I would like to construct example(s) of (u,v)-clopen compact BS. 

I've proved the following theorem using model-theoretic techniques, namely ultraproducts: A continuum is locally connected if every semi-monotone mapping onto it (from another continuum) is monotone. Monotone means the usual thing; semi-monotone means that every subcontinuum K of the range space is the image of a subcontinuum in the domain space, which contains the pre-image of the interior of K. The part that uses ultraproducts is where we want to prove that non-locally connected implies being the image under a semi-monotone map that isn't monotone. Basically, I'm wondering if someone has any insights into obtaining a new proof more palatable to a continuum theorist. (E.g.: start with a non-locally connected metric continuum Y and directly construct a metric continuum X and a semi-monotone f:X->Y which is not monotone.)

How many topologies can one define on a particular set?