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From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Sun Feb 05 2012 - 18:24:40 CST
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Hi.
You may try swiss param (http://swissparam.ch/)
The output file generated contains: *.pdb, *.psf, topology and parameters files in Gromacs or Charmm formats.
Of course, if you need accurate force fields you must to improve topology (bonds, distances and charges) using Gausian Software.
Regards,
Flavio
--- On Sun, 2/5/12, Rajan Vatassery <rajan_at_umn.edu> wrote:
> From: Rajan Vatassery <rajan_at_umn.edu>
> Subject: vmd-l: PSFGEN and Reading Bonds from PDB Files
> To: vmd-l_at_ks.uiuc.edu
> Date: Sunday, February 5, 2012, 8:13 PM
> Hi All,
> I am looking for a way to avoid creating
> a topology file whenever I
> need to create a new PSF. For example, my current need is
> for a PSF for
> oleic acid. I can easily create a pdb file, but the creation
> of a PSF is
> substantially more time-intensive. Currently I would need to
> make a
> topology file, which although is not terribly difficult, is
> not used
> after the creation of the PSF.
> My hope is that there is some way that I
> can use the bonds given in the
> pdb file to produce the essential details that PSFGEN needs
> to then go
> on to writing the angles and dihedrals. As it is now, if I
> try to create
> anything in terms of a segment for writing (segment U {pdb
> Oleate.pdb}),
> I get the usual:
>
> unknown residue type
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to
> start over.
>
> because I haven't given a topology file to PSFGEN.
> My impression is that during the normal
> PSF creation from a topology
> file, PSFGEN calculates the angles and dihedrals from only
> the list of
> bonds that are given in the topology file. So my question
> stated in
> another way is, can I trick PSFGEN into reading the bond
> list from the
> PDB file? I would even rather write the first part of the
> PSF (atoms and
> bonds) if I could get the angles and dihedrals automatically
> generated.
>
> Thanks in advance,
>
> rajan
>
>
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