VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 07 2017 - 11:14:14 CST

On Tue, Feb 7, 2017 at 11:57 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Axel,
> Good points. I read the email so quickly I missed that the input was
> solely a PDB and nothing else. Maybe using the AutoPSF plugin would be
> useful in this particular case?
>

not sure. this looks like a carbon nanotube, and topotools works fine on
those, if the original guessed bonds are correct.
the nanotube plugin in VMD uses topotools as well, but it also applies
required force field related settings (for CHARMM that is).

​axel.​

>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Feb 07, 2017 at 11:45:30AM -0500, Axel Kohlmeyer wrote:
> > On Tue, Feb 7, 2017 at 11:13 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > > Hi,
> > > What version of VMD are you using? The PSF plugin in recent versions
> > > of VMD does support writing of angles/dihedrals/impropers, and even
> > > cross-term maps. I would suggest that you try running VMD 1.9.3 and
> see
> > > if that cures your problem, since it seems likely that you are using an
> > > out-of-date version of VMD.
> > >
> >
> > ???i don't think that is the problem.
> >
> > the issue is more likely, that the .pdb file will only contain
> coordinates
> > and VMD will only guess bonds when loading the file.
> > it will not try to determine angles, dihedrals or beyond, since those are
> > not required for visualization. this also should be checked carefully,
> > since the heuristics in VMD do not always get everything right (after
> all,
> > they are only heuristics).
> >
> > you can try to guess angles and dihedrals via Tcl scripting using the
> > topotools plugin???. however, that will not produce a valid .psf file
> unless
> > you also assign the proper atom types, residue names, partical charges
> (if
> > any) etc. according to the requirements of the specific force field you
> are
> > using.
> >
> > axel.
> >
> >
> >
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Tue, Feb 07, 2017 at 04:09:33PM +0330, Statics Eng wrote:
> > > > Hi all
> > > > I have a question about obtaining Topo file from a pdb file of Guess
> view
> > > > software by VMD. I need atoms/bonds/angles/dihedrals but I only can
> > > obtain
> > > > atoms and bonds from "animate write psf CNT.psf" command in VMD.
> > > > Indeed I should function a CNT by Amin group and I do this in Guess
> view
> > > > software. Then I need Topo file and I want to obtain it from VMD but
> I
> > > only
> > > > can obtain atoms and bonds.
> > > > Please help me.
> > > > Thanks
> > >
> > >
> > > --
> > > NIH Center for Macromolecular Modeling and Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > > http://www.ks.uiuc.edu/Research/vmd/
> > >
> > >
> >
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> > College of Science & Technology, Temple University, Philadelphia PA, USA
> > International Centre for Theoretical Physics, Trieste. Italy.
>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.