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# General Topology - Science topic

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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.
I remember I read some years ago a paper on semi-open sets, containing also a definition of semi-continuity(wich use the semi-open set notion):
A function f:X->Y (X,Y topological spaces) is semi-continuous(globally) iff
f-1(D) is semi-open in X for all D open in Y.
Now, looking at your comment, I wonder if:
1. The notion of semi-open set can be exploited in Measure Theory, in the sense that some theorems from Measure Theory can be more simple formulated and used?
2. The demicontinuity of operators T:E->F(E,F - Banach spaces) has connections with general topological notion of semi-continuity of functions(above defined)?
I must point out that an operator T:E->F(E,F - Banach spaces) is demicontinuous at point z in E if for all sequence (xn) converging in norm to z(in E) we have T(xn) converges weakly to T(z). T is globally demicontinuous if T is demicontinuous at every point of E.
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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 ?
It seems you have two [ defaults ] section, one in forcefield.itp and other in charmm36.itp file. This section should be included in the main topology file or in forcefield file.
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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?
Hi
You can try the ATB server ( Automated Topology Builder (ATB) and Repository )
But before that what type of error did face through MD? because PRODRG is a good server to generate topology, did you try to fix the structure first? then proceed?
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For MD simulation of protein-ligand, it is important to generate topology file of ligand.
Salamu Alaikum
you can use the PRODRG Server (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg). It is an error-free and quick generator that you may use.
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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.
Your work sounds like you want a nonbonded metal force field parameter.
Try using frcmod.ions1lm_1264_tip3p
I have seen the frcmod.ionsjc_tip3p file in the following link:
> And this force field file for monovalent ions. you have not mentioned which oxidation state you want (Fe2 or Fe3).
>Don't mix up the water model force field file using a different set of force fields. If you want TIP3P then only the same force field file you used or vice-versa for SPC/E.
Hopefully, it will work.
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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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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.
Dear Anuththara
You can generate the system using the amber force field.
If you want non bonded force field parameter then you can be used amber.
It already has magnesium(+2) force field parameter.
If you want bonded force field parameter then you can use MCPB.py.
Look into the tutorial.
Hopefully, it will help.
Best regards
Aashish
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Uses in applied mathematics and computer sciences
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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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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 ?
Thank you !
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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)
Muhammad Ali Yes I can give it a try. The question is I don't know if the outcomes are right or wrong. Fortunately, I have recently found a paper [Identification of a New Allosteric Binding Site for Cocaine in Dopamine Transporter] using this method, maybe it is ok to do so.
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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.
I am going to use the GAFF force field for other, less problematic molecules, therefore I wanted to get to know the nature of the problem and check if it would interfere further.
Thanks for the suggestion, I will try other force fields.
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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
Thanks a lot for the quick reply, really appreciate it the link to SEED was really helpful. I guess it was a problem with the CHARMM stream file preparation, which was resolved with SEED.
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Dear colleagues. The text of the question is available in the attached image or pdf-file.
Sincerely, Yaroslav Grushka.
Dear Professor,
You may want to consult the following manuscript:
Regards
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who's registered
as an endorser for the math.GN (General Topology) subject class of
arXiv.
Yes, you can submit your article to arXiv. It is very good and most of the researchers use it for submission their articles/manuscripts.
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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.?
Don't use PRODRG. It is wildly inaccurate and not suitable for reliable simulations.
Repeated parameters with CGenFF indicate either your parametrizing the same dihedral multiple times (don't do this, just come up with one set of parameters) or the dihedral parameters already exist in the force field, in which case you should remove your parameters from the .prm file and use the ones in ffbonded.itp.
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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
Excuse me, sir. I am doing silver or gold related simulations with cpmd , but i want to expand my system by using the MD method. I had tried to get the topology files for Ag or Au from prodrg and others , but failed. Can you give me some information on how to carry out nanoparticle simulations with gromacs ? Thank you
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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.
Doesn't count, since everyday there is a new structure generalized topology is created such that fuzzy topology, multi topology, soft topology, supra topology, weak structures, minimal structures, ordered topology, fuzzy rough topology, multi fuzzy topology, soft multi topology, ...etc.
Regards.
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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.
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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
Hi Raghav
ACPYPE generate the topology and parameter file for the small molecules with force fields like AMBER99SB or GAFF. The topologies generated according to the format of GROMACS (<file name>_GMX.itp, <file name>_GMX.top, <file name>_GMX.gro), OPLS (<file name>_GMX_OPLS.itp and same), CNS (<file name>_CNS.top and same). Thus without breaking the compatibility of the force field, the topologies generated can be used in AMBER force field or OPLS force field as ported in the GROMACS.
In your case, you have selected the itp file of the GROMACS format and top file of the OPLS format.
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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.
Parametrize the doubly-deprotonated histidine as a new residue.
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Digital topology, space set topology
can we do collobration dear dr adiya. I will so happy collabrate with u
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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
You don't need to parametrize Mg2+. Every force field already has parameters for it, and the parameters for ATP should not depend on Mg2+ at all, anyway, as doing so would create non-transferable parameters.
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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).
The notation:
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
Giorgio Pattarini I've corrected: \mathfrak{A} -> \mathfrak{F}.
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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
These are the force fields that natively support ATP in GROMACS:
$grep "ATP" *.ff/*.rtp charmm36.ff/merged.rtp:[ ATP ] gromos43a1.ff/aminoacids.rtp:[ ATP ] gromos43a2.ff/aminoacids.rtp:[ ATP ] gromos45a3.ff/aminoacids.rtp:[ ATP ] gromos53a5.ff/aminoacids.rtp:[ ATP ] gromos53a6.ff/aminoacids.rtp:[ ATP ] gromos54a7.ff/aminoacids.rtp:[ ATP ] As stated above, if you want parameters for other force fields, you will need to obtain them from another source. • asked a question related to General Topology Question 2 answers 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>? Relevant answer Answer drug like molecule... meanwhile, I have solved this issue. thank's • asked a question related to General Topology Question 7 answers 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. Relevant answer Answer Hello everyone, Luckily i solved the problem like this: Before installation of Ambertools, we have to install conda platform which allows you to install ambertools and other software packages. but it is compiled with python platform. System requirements 32- or 64-bit computer. For Miniconda—400 MB disk space. For Anaconda—Minimum 3 GB disk space to download and install. Windows, macOS or Linux. Python 2.7, 3.4, 3.5 or 3.6. 2) In your Terminal window, run: bash Anaconda-latest-Linux-x86_64.sh Follow the prompts on the installer screens. If you are unsure about any setting, accept the defaults. You can change them later. To make the changes take effect, close and then re-open your Terminal window. Now download the ambertools: Binary Distribution via Conda: conda install ambertools=18 -c http://ambermd.org/download/ambertools/conda ACPYPE installation: git clone https://github.com/alanwilter/acpype.git Enter in the acpype folder and type ln -s$PWD/acpype.py /usr/local/bin/acpype the ACPYPE program can now be used.
Thats it.
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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?
.
if you can make sense of the following thread :
(i'm having hard time with it ... but thanks for the question ; had me review a pile of long-forgotten concepts !)
.
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I am trying to compute eutectic solvent. ERROR 1 [file darginine.itp, line 65]: Atomtype HS14 not found
HS14 is a type of hydrogen which generates Automatic topology builder (ATB server). You can add C6 and C12 parameters to your force field or just use ATB based force field 54a7.
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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?
Zhaoxi Sun I tried mimicking the workflow in the Crystal Simulation tutorial from the AMBER website, but the program addToBox fills my crystal lattice only, and I end up with a really cramped and jumbled setup of 602 naphthalene molecules squeezed into the unit cell of pentacene. Is there a way I can tell AddToBox to add solvent outside the crystal lattice but within another well defined boundary
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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
James F Peters, Artur Sergyeyev Thank you very much Professors for your king suggestions. However, I am looking for where I can get a free e-copy of the book.
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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
There are online servers for example, ATB server, which shall provide you with the gromacs compatible topology files (all-atom/ united atom). After that you can edit the file if you want to specifically tune some interactions. Or you can use antechamber package that comes with AMBER tools to generate the topology for AMBER and later convert it using a simple python script (available online) in gromacs compatible format. You can directly ue AMBER for your simulation as well.
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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.
you can use two tools in gromacs:
and
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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.
As I mentioned in my email when you asked me (and for the benefit of the RG community I'm posting here), you're using an outdated version of GROMACS that has a broken force field file. Use version 5.1.5 or newer.
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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??
Dear Barış
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The question details are contained in the attached pdf file.
W.H. Young, “A note on monotone functions,” The Quarterly Journal of Pure and Applied Mathematics (Oxford Ser.) 41 (1910), 79–87.
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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?
To solve the "Invalid structure file" problem, you shuold check the pdb text file (to avoid error in the structure file).
Thanks.
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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)?
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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?
Check the [dihedral_type] section of your itp/topology file thoroughly. This error occurred to me once when I had more than one numbers in the function column. Make sure there is just '1' in the dihedral function type column.
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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.?
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?
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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:
pdb2gmx -f WILD0MODEL.B99990001.pdb -o conf.pdb
Where I have tried with three following force fields and water model
1.Amber99sb
2.OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
3.CHARMM27 all-atom force field (with CMAP) - version 2.0
1.TIP4P TIP 4-point, recommended
But i get the following error:
ERROR:
Writing topology
Processing chain 2 'A' (11 atoms, 1 residues)
Warning: Starting residue BGC505 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.1
Source code file: /Users/Mahesh/Applications/gromacs-4.6.1/src/kernel/resall.c, line: 642
Fatal 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.
Your example is a non-covalent ligand, so the story keeps changing here. The approach outlined in your last reply is for a non-covalent ligand, which is a different approach entirely. As for the last question, things can't magically disappear. Either the species is present in the coordinates and topology or it is not.
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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?
dear subrata this is corresponding to csazar generalized topology of course u can check it ZF or AC system
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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)
A point from the underlying set with a single parameter assume single value.
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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?
This is a good question with many possible answers.
Soft topology is introduced in
To answer this quetion, we need to consider the possibility of a pullback operation,, in which a structure in soft topology can be replaced by a structure in general topology. Recall that a soft set is a set of ordered pairs (x,fA(x)), where fA(x) is anj approximation function and x is an uncertain that is approximated using parameters in A. Nonempty sets in a general topology do not depend on an approximation function. From this, soft sets cannot be pulled back to ordinary sets. Since the properties of soft topology are defined in terms of soft sets, such properties have no counterpart in generAl topology.
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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.
Dear Dr. Bhowmik
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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.
Boundedness is a topic of bornology. You can introduce many bornologies on your spaces, so you will get many notions of a bounded set.
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Am more interested in answers relating to general topology.
This is an excellent question.
For a good overview of connectedness in topology, see Section 2.4 in
For a thoroughgoing look at connectedness as well as disconnected in topology, see
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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??
As far as I understand the question the problem is that the triangles in an STL file are not connected to each other. The vertices are repeatedly stored for each triangle.
Here is one way how to create a truly connected mesh: The best representation for triangles is to use indices to a list of vertices. So, at first you can just read in everything and append all the vertices into one big vector. For the triangles you just enumerate indices to point to the corresponding vertices consecutively. In a next step you need to identify identical vertices. Based on a small threshold you group vertices with the 'same' coordinate. Here it is useful to create a map from the old indices to the new ones. If you are using the map the final step is to loop over all triangles and update their indices according to this map. Now, you have triangles (and possibly edges) sharing vertices. This should help with finding the connectivity information you are looking for.
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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?
To generate parameters for a new molecule in an existing force field, you need to familiarize yourself with the parametrization protocols of that force field. For OPLS, this typically involves some QM calculations for charge assignment and bonded parameters based on relative energies in the gas phase; empirical refinement follows based on liquid properties.
A DMSO model already exists in OPLS-AA in GROMACS, though, so I don't understand your assertion that it doesn't work. The residue is clearly labeled "DMSO" in aminoacids.rtp but does have a cautionary note about the fact that the parameters are not thoroughly validated. But perhaps those can be a starting point for additional optimization, to save you some of the laborious work of coming up with parameters de novo.
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Is there any topological space which are not singletons e-closed?
There is for any fixed point $y \in X$, a general topology consists of all subsets containing $y$ union the empty set.
In that topology, you will find for the subset $H = X \minus\{y\}$, that:
$H \not\subseteq (cl int H \cup int cl H) = \phi$, that is, H is not e-open and thus $\{y\}$ is a singleton but not e-closed in your sense.  Note that $int H = \phi$ and $cl H = H$ whenever $y \not\in H$.
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As like compactifications of generalized (or classical) space can we define Lindelofization of generalized (or classical) topological spaces?
Why don't you try the same idea as for the Alexandrov compactification? There one considers a locally compact space, one adds an extra point, and one defines the new neighborhoods of the extra point as the complements of the compact subsets of the space (together with the extra point). It is an easy exercize to show that the new space is compact.
So you must define local Lindelöf spaces, where any point belongs to an open set possesing a Lindelöf closure. We add an extra point and we define its neighborhoods as complements of all closed Lindelöf subsets. At the first sight it looks to work, but maybe one has to add more conditions (both to premises and conclusion) in order to make the statement interesting and/or useful.
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here Cp-pointwise topology, C(X) topological ring with usual operations and supremum norm
More precisely:     Cp(X) is separable iff X is separably submetrizable space.
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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
... Hum, I thought a little more and now I see that "Compact T2 is T4" in fact holds in ZF. We do not have to pick exactly one open neighbourhood for every point of the closed sed; let us take them all, and then compactness make things go down to finite open sets and everything is OK. So, as usual, we first prove that compact T2 are T3 (in ZF, with this argument of picking all possible open sets for every point) and then repeat the argument for compact T3 is T4. Very nice ! Thank you.
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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?
0. All relation closure algorithms proceed along the following lines:
convert to directed graph
basically it is a shortest path problem
solve in =< O(v^3 logv)
(v being no of vertices in graph)
(see a good book on algorithms - here the problem is of improving algorithms)
___________________________________
Some extensions of confluences are characterized in the 1st paper (120). Suppose the extension of S is S*, then your problem would be to define a nice map
f :S* --> S and get the closure as a quotient of S*.
(this would be a paper)
In the 4th paper, they consider closures of relations which turn out to be confluences.
(might be usable)
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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.
Eric is right. I am a finite element person and don't know much about geometry which is tooooo hard for me.  What we are doing is to divide a 3D convex polyhedron domain to many small convex polyhedrons shared faces. Then define piecewise polynomials associated with these partitions (or meshes) to approximate solutions of PDE.
Let me make it straight that for my situation, the formula is
n_0 − n_1 + n_2 − n_3 = −1.
with
n_0=total  number of interior vertices,
n_1= total number interior edges,
n_2=total number interior faces
n_3=total number polyhedrons (not just interior).
Is the above statement right?
Many thanks to Stam and Eric.
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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
That doesn't make any sense. Periodicity is normal; there is no "outside" of a box with PBC.
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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=pr, 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∣=qk for some integer k.
I would like to also recommend chapter 2 ("Global Fields") of the classical book 3Algebraic Number Theory", Cassels & Fhröhlich ed., Acad. Press 1969, which gives a compact and complete account of the subject. Concerning your specific question, see especially §7, p.50
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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.
ATB is a pretty good server, but always evaluate the parameters you get from any automated process. GROMOS parametrization relies on empirical assignment of parameters, and groups are very transferable, so generally any irregularities are easy to spot.
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Generalized topology, Compactifications
You can find it below as attachment file.
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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.
There are also restrictions on the notion of "open set."  In addition to open sets that are  closed as well (clopen sets), there are the regular open sets:  one of these is equal to the interior of its closure.  Clopen sets are regular open, but not conversely (as the complement of a point in--say--the real line will attest).  There are also the dense open sets, of importance in the study of Baire category issues. Obviously a dense open set is regular open iff it is not a proper subset. G-delta sets are also of interest in the Baire category context, as well as in analysis and descriptive set theory.  They are a kind of "generalized open set," being countable unions of open sets.  I'm not sure this is of any help, so I'll stop here.
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I want to know relation of these operators  whether these are equal or subsets
This is a good question.   Quite an interesting question, if we consider the possibility of pre-closure spaces.
Pre-closure space theory is introduced in
M.J. Schroeder, Modification of pre-closure spaces as closure-interior operations of the lattice of pre-closure operators, Akita Int. University, Akita, Japan, 2010:
The story starts on page 150, where subsets are defined relative to a partially ordered set F(S), which stands for the set of all operators on a given set S.    The  partial order defines a rich structure that makes the reconstruction of large portions of a closure space.   See the Lemma at the top of page 152.
The distinction between pre-closed and semi-closed is given in
T.S.I. Mary, P. Thangavelu, On regular pre-semiclosed sets in topological spaces KBM Journal of Math. Sci. & Computer Applicaitons l, 2010, no. 1, 9-17:
See Definition 2.2, page 10 for the distinctions.   See, also, Proposition 3.2, page 12.
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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?
Here's how I ran across the problem above: as is well known, if X is a compact Hausdorff space and a, b are in separate components of X, then a and b are in separate quasicomponents of X.  In my case, start with a continuum X (= connected + compact + Hausdorff) with the property that whenever a and b are distinct, there is a third point c such that a and b lie in separate components of X-{c}.  Can we always conclude that a and b lie in separate quasicomponents of X-{c}?  The answer is YES.
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I could not find definition of a bounded set in a general topological group in any book. Any help will be appreciated.
The definition of bounded subset in a topological group has many variants.  You may have much information about this question in the paper:
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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
You need to have the topology file first.....then.... 1)read coordinate of your mol2 file ...2) set resname according to topology file......3)write a new pdb file ...3)and run psfgen.....
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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
Dear Venkat,
We used the MMFF94x force field for the computation of beta-peptides.
Best regards
István
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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.
Dear Irakli,
Concerning your question, I can only note that if \Cal R is a relator
(family of relations) on set X then \Cal R and \Cal R^{-1} induce two
generalized topologies on X. So X becomes a generalized
bitopological space.
Moreover, if \Cal R is a relator on X to Y, then the relator space
(X, Y,)(\Cal R) has to be clalled properly compact if for each
R \in \Cal R there exists a finite subset A of X such that R[A]=Y.
This definition is, is in my opininion, quite constructive.
By using appropriate closure operations on relators, you can get
several old an new compatness concepts. For some ideas in this
respect, see my earlier papers:
1. Uniformly, proximally, and topologically compact relators,
Math. Pannon. 8(1997), 103--116.
2. Lebesgue relators, Monatsh. Mat. 110( 1990), 315--319.
Sincerely yours,
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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.)
There are many incarnations of what is known as a continuum, e.g.,
1. continuum in set theory: the set R.
2. coninuum in topology: Hausdorff space. Distinct points belong to disjoint neighbourhoods.
I can suggest an approach in terms of a Hausdorff space. Let x and y be distinct points in a metric Hausdorff space X endowed with an Efremovic proximity relation. Let Nx, Ny be disjoint neighbourhoods of x, y, respective, where, for example,
$N_x = \left\{y\in X: d(x,y) < \varepsilon\right\},$
with $\varepsilon > 0$ and $d$ is the standard distance between x and y. Then Nx and Ny are connected, provided
$\mbox{cl}(A) \cap \mbox{cl}(B) \neq \emptyset.$
In other words, cl(Nx) and cl(Ny) have at least one point in common and cl(Nx) and cl(Ny) are then adjacent to each other. In other words, Nx and Ny are disjoint but cl(Nx) and cl(Ny) are not disjoint. If every pair of closures of disjoint neighbourhoods is connected in a subspace of X, then the subspace is locally connected.
One question to consider is this: what if Nx = {x} and Ny = {y}. Does the above line of reasoning work?
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