VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 15 2010 - 08:59:42 CDT

On Tue, Jun 15, 2010 at 9:49 AM, Rabab Toubar <rtoubar_at_yahoo.com> wrote:
>
> 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?

of course:

animate write psf myfile.psf

> 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.

one possible alternative (untested):

#load .gro and .psf file into vmd
set mol1 [mol new myfile.psf waitfor all]
set mol2 [mol new myfile.gro waitfor all]
set sel1 [atomselect $mol1 all]
set sel2 [atomselect $mol2 water]

# merge selections into new molecule.
package require topotools
::TopoTools::selections2mol "$sel1 $sel2"

# write out new molecule
animate write psf combined.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.
> 

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