VMD-L Mailing List

From: caterinabernini_at_unisi.it
Date: Tue Jan 06 2009 - 11:40:15 CST

Dear VMD experts,

I have run a MD simulation with NAMD 2.6 of a protein in a water box and I
obtained an equilibrated structure. Now I would like to use this structure
(with hydrogens) as a starting point to do another MD simulation in which
one of the amino acid residue (Trp) is deprotonated and the one next to it
(Glu) is protonated. In order to do that, I made a glup patch to Glu
residue and I wrote a new psf and a new pdb file. Then, I tried to
eliminate the tryptophan proton using TkConsole:

> set sel [atomselect top "not index x"]
> $sel writepdb "newpdb".pdb
> $sel writepsf "newpsf".psf

Doing that, the psf and pdb files have the same numeration but the output
of the MD simulation does not make sense (I can see atoms collapsing one
upon each other!).

Does anybody can help me?

Thank you in advance for your suggestions,
Caterina 

-- 
Caterina Bernini, Ph. D. Student
Department of Chemistry
University of Siena
Via A. De Gasperi, 2
53100 Siena - Italy