VMD-L Mailing List

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Tue Jun 15 2010 - 08:49:31 CDT

I need the .psf file as we have in house codes used for analysis and these use .psf and .dcd as in case of NAMD.

I tried to load the .gro or .pdb files and save coordinates as psf, but this is not an option in the drop down menu in vmd; is there a way I can do it in tcl?

I do have disulfide bonds- if this what you meant by unusual bonds.

In the meantime I will try in gromacs to get the .top file from the .gro and see if this would work to get the .psf.

Thanks
Rabab Toubar

--- On Tue, 6/15/10, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

From: Axel Kohlmeyer <akohlmey_at_gmail.com>
Subject: Re: vmd-l: top2psf.tcl
To: "Rabab Toubar" <rtoubar_at_yahoo.com>
Cc: "vmd-l" <vmd-l_at_ks.uiuc.edu>
Date: Tuesday, June 15, 2010, 9:29 AM

On Tue, Jun 15, 2010 at 9:21 AM, Rabab Toubar <rtoubar_at_yahoo.com> wrote:
>
> Thanks Axel for your reply
>
> My .top file has no waters, as it is the initial .top file I get using grompp, and it has a total of 357 atoms (attached).
>
> The md gro file has 11632, and it contains waters.

well, you cannot load multiple files into the same VMD
"molecule" that have different number of atoms.

> I can visualize the molecule using .pdb or .gro file with the .trr, but I need to have a psf files for further analyses, so can I possibly include waters in the top file? or may be delete it from the .trr file?

what exactly do you need the .psf file for?

the one generated from the .top file is only minimal
and only contains the bonding information and atom
names. that is suitable for visualization in VMD, but
not much more. in most cases, you can generate the
same kind of file by loading a .gro or .pdb file and saving
the result in a .psf file. only if you have unusual bonding,
you'd need to read it from the .top file.

cheers,
    axel.

>
> Thanks
> Rabab Toubar
>
>
> --- On Sun, 6/13/10, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> Subject: Re: vmd-l: top2psf.tcl
> To: "Rabab Toubar" <rtoubar_at_yahoo.com>
> Cc: "vmd-l" <vmd-l_at_ks.uiuc.edu>
> Date: Sunday, June 13, 2010, 8:19 AM
>
> > However when I load the psf file in vmd, I got the following:
> >
> > "psfplugin) WARNING: no angles defined in PSF file.
> > psfplugin) WARNING: no dihedrals defined in PSF file.
> > psfplugin) WARNING: no impropers defined in PSF file.
> > psfplugin) no cross-terms defined in PSF file.
> > Info) Analyzing structure ...
> > Info)    Atoms: 357
> > Info)    Bonds: 365
> > Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
> > Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
> > Info)    Residues: 36
> > Info)    Waters: 0
> > Info)    Segments: 1
> > Info)    Fragments: 1   Protein: 1   Nucleic: 0"
>
> that is to be expected after the debug output from above.
>
> > And when I load the trr file from GMX, I get the following:
> >
> > "ERROR) BaseMolecule: attempt to init atoms while structure building in progress!
> > ERROR) Invalid number of atoms in file: 11632
> > Info) Using plugin trr for coordinates from file /home/Desktop/gmx/pr_md_1.trr
> > ERROR) Incorrect number of atoms (11632) in
> > ERROR) coordinate file /home/Desktop/gmx/pr_md_1.trr
> > Info) Finished with coordinate file /home/Desktop/gmx/pr_md_1.trr."
>
> either the .trr file doesnt match the .top file, or there is something
> else wrong, that is impossible to debug without having access
> to those files. have you tried loading a matching.gro file?
> how many atoms does it have?
>
> cheers,
>       axel.
>
> > PS I am using the preprocessed top file like Axel suggested in an earlier post
> >
> > Any suggestions would be much appreciated
> > Thanks
> > Rabab Toubar
>
>
>
> --
> Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
> 

--
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.