VMD-L Mailing List

From: Anurag Sharma (Anurag.Sharma_at_my.ndsu.edu)
Date: Wed Apr 17 2013 - 23:33:21 CDT

Hi John,
     
    Thanks for the suggestion. It works. I generated psf and pdb directly after deleting the water atoms. I got all the no. correct.

Cheers!!

Anurag Sharma

________________________________________
From: John Stone [johns_at_ks.uiuc.edu]
Sent: Wednesday, April 17, 2013 9:51 PM
To: Anurag Sharma
Cc: Josh Vermaas; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: No bonds in the generated psf file

Hi,
  After you delete some of the waters, you need to generate
a PSF at that point as well as the PDB. The PDB file does not
contain any bond information. This may be related to your problem.
In order to help you further, you will need to specify _exactly_
what steps you have performed by showing what commands you have run.
The descriptions you've given up to this point aren't good enough
to determine why you're having this problem. Show us exactly what
sequence of commands you ran, and then we can help you solve it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 18, 2013 at 02:25:30AM +0000, Anurag Sharma wrote:
> John,
>
> I had the psf and pdb files of my solvate model. I deleted some of the water molecules and save the coordinates of rest of the model in pdb. I checked the no. of bonds in this pdb and I got the correct no. Then I used topo guess command to get bonds/angles/dihedrals/impropers. Then I again checked all of these parameters by using topo num command. This shows me correct no. Then I used animate write psf command. The psf file generated from this has everything other then bonds.
> I am using VMD 1.9.1.
>
> Thank you
>
> Anurag Sharma
>
> ________________________________________
> From: John Stone [johns_at_ks.uiuc.edu]
> Sent: Wednesday, April 17, 2013 9:07 PM
> To: Anurag Sharma
> Cc: Josh Vermaas; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: No bonds in the generated psf file
>
> Anurag,
> How did you get the other data into the VMD molecule? If you read
> in angles/dihedrals/impropers, then you should have had bonds also.
> If VMD had to "guess" the bonds, then it won't save them when you
> write a PSF. If the bonds were loaded from a file, then indeed they
> should be saved when you write a PSF. What version of VMD are you
> running?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Apr 18, 2013 at 01:59:28AM +0000, Anurag Sharma wrote:
> > Hi John,
> >
> > I am using VMD command and I am getting all the data which is in the VMD molecule other than bonds.
> >
> > Thanks
> >
> > Anurag
> >
> > Sent from my iPhone
> >
> > On Apr 17, 2013, at 8:52 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:
> >
> > > Hi guys,
> > > I think there's some confusion in this discussion.
> > > The "animate" command is a VMD command (not psfgen), and the
> > > only data that it saves is whatever data is in the VMD molecule you're
> > > writing from. This is not the same as the structure that one builds
> > > in psfgen. If you're building a molecule in psfgen, then you have
> > > to use the psfgen "writepsf" and "writepdb" commands, and you
> > > would not use any of the VMD commands to write a structure built inside
> > > of psfgen.
> > >
> > > Cheers,
> > > John Stone
> > > johns_at_ks.uiuc.edu
> > >
> > > On Wed, Apr 17, 2013 at 06:32:56PM -0500, Josh Vermaas wrote:
> > >> Hmm, you appear to have stumbled into a bug with how psfs are written, as
> > >> my tests show that it fails to write them out too if I use guessbonds. If
> > >> you are just trying to delete waters, the psfgen userguide
> > >> (www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf) has a handy little
> > >> section devoted to this very topic, and you'd save yourself quite a bit of
> > >> heartache until someone fixes the psf writer.
> > >> -Josh
> > >>
> > >> On 04/17/2013 05:52 PM, Anurag Sharma wrote:
> > >>
> > >> Josh,
> > >>
> > >> I have tried the topo guessbonds command. It gave me the right no. Of bonds which I verified with topo numbonds but when I used animate write psf command and generate psf file. There are no bonds mentioned in that psf file ( all other parameters are present). That means the problem I am facing is in animate command.
> > >> I am deleting water molecules from inside the tube here.
> > >>
> > >> Thanks
> > >>
> > >> Anurag Sharma
> > >>
> > >> Sent from my iPhone
> > >>
> > >> On Apr 17, 2013, at 5:42 PM, "Josh Vermaas" <vermaas2_at_illinois.edu> wrote:
> > >>
> > >>
> > >> If you are satisfied with the number of other terms present in the psf, all you'd need to do is add a line like:
> > >> topo guessbonds
> > >> and then write the psf file with animate. I'd be very careful though, as psfs are easy to screw up unintentionally when building them by hand. As others have pointed out on this list, there is a perfectly serviceable nanotube builder (http://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/) and the usual solvation schemes (http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/) will get you a nanotube in water without needing to rebuild bond tables.
> > >> -Josh
> > >>
> > >> On 04/17/2013 02:54 PM, Anurag Sharma wrote:
> > >>
> > >> Hi,
> > >>
> > >> I am working with a solvated Carbon nanotube model. I have deleted some of the water molecules in the model and try to generate psf file for this new model using topo tools. I used animate write psf script to create this psf file. But in the generated psf file the bonds are missing (0 bonds). Though when I used guess bonds and then numbonds in tcl it shows the correct no. What could be the possible solution for this problem. Please suggest.
> > >>
> > >> Angles, dihedrals and impropers are present in the generated psf file. All other parameters are also present. Only bonds are missing.
> > >>
> > >> Thank you
> > >>
> > >> Anurag Sharma
> > >
> > > --
> > > 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/
> > >
> >
>
> --
> 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/ 

--
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/