distorsion in hydrogens added

From: regafan_at_usc.es
Date: Tue Nov 21 2006 - 05:47:58 CST

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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