VMD-L Mailing List

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Tue Jun 15 2010 - 08:21:19 CDT

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.

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?

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.