VMD-L Mailing List

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Sun Jun 13 2010 - 05:59:28 CDT

Hi,

I used top2psf and it seems that I got the psf file correctly:

"perl top2psf.tcl -p pr_g2psf.top -o pr_g.psf

converting from gmx top.... pr_g2psf.top

psf_res_offset............. 0

reading input files........
appending to............... pr_g.psf
last residue found.........
DEBUG - starttop........... 2
DEBUG - finishtop.......... 359
DEBUG - number of atoms.... 357
DEBUG - number of bonds.... 365
input files read...........

converting................. done
last atom read............. 357 OM O2
from residue............... 36 LYSH"

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"

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."

PS I am using the preprocessed top file like Axel suggested in an earlier post

Any suggestions would be much appreciated
Thanks
Rabab Toubar