VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 07 2017 - 10:57:52 CST

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?

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 out-of-date version of VMD.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/