Re: distorsion in hydrogens added

From: Jerome Henin (
Date: Tue Nov 21 2006 - 09:47:17 CST

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.

On Tuesday 21 November 2006 06:47, 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)

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