From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Tue Nov 21 2006 - 14:25:05 CST
IN your file, all leucine HGs have wrong coordinates. This problem has
happened before, Peter Freddolino explains it there:
Using recent CHARMM topology files (c31b1 and following) with the latest
version of psfgen should give a good result.
On Tuesday 21 November 2006 14:39, regafan_at_usc.es wrote:
> the main problems are in the residue "PRO", here the angles are really
> distorted in some cases.
> I send you a pdb of my protein after creating the psf.
> What is also really extrange is that a minimization of the protein
> does not correct the hydrogens in these residues, being the resultant
> structure perfectly stable.
> In response to your question, psfgen does not print any warning in the
> generation of the structure
> Thanks a lot for your help
> Rebeca García Fandiño
> Postdoctoral student
> Parc Cientific de Barcelona (Spain)
> Citando Jerome Henin <jhenin_at_cmm.chem.upenn.edu>:
> > Hi,
> > Are all hydrogens wrong or just a few? In what residues?
> > Also, does psfgen print warnings or errors when generating the structure?
> > It might also be helpful if you post a small gzipped pdb file
> > containing, say,
> > one or two residues with these distorted hydrogens.
> > Jerome
> > On Tuesday 21 November 2006 06:47, regafan_at_usc.es wrote:
> >> Hello,
> >> I want to do a simulation of a protein using NAMD and CHARMM force
> >> field.When I create the psf file for a protein from a pdb structure
> >> without hydrogens (from XR) I get a resultant structure where the
> >> hydrogens added (guesscoord) are very distorted (mainly the angles).
> >> When I minimize this structure, this distorsion does not disappear,
> >> but incredibly, the energy is stable after some steps. If I use this
> >> resultant structure for equilibration, RATTLE errors appear.
> >> Has anybody ever had this problem?
> >> Thanks a lot in advance!
> >> Rebeca García Fandiño
> >> Postdoctoral student
> >> Parc Cientific de Barcelona (Spain)
> >> regafan_at_usc.es
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