From: Axel Kohlmeyer (
Date: Tue Jan 06 2009 - 12:33:37 CST

On Tue, 6 Jan 2009, wrote:

CB> Dear VMD experts,

ciao caterina,

CB> I have run a MD simulation with NAMD 2.6 of a protein in a water box and I
CB> obtained an equilibrated structure. Now I would like to use this structure
CB> (with hydrogens) as a starting point to do another MD simulation in which
CB> one of the amino acid residue (Trp) is deprotonated and the one next to it
CB> (Glu) is protonated. In order to do that, I made a glup patch to Glu
CB> residue and I wrote a new psf and a new pdb file. Then, I tried to
CB> eliminate the tryptophan proton using TkConsole:
CB> > set sel [atomselect top "not index x"]
CB> > $sel writepdb "newpdb".pdb
CB> > $sel writepsf "newpsf".psf

please note, that the resulting .psf file is only useful
for visualization. there is a _big fat warning_(tm) on the
VMD console to that extent. the psf file is lacking the angle
and dihedral information.

you have to use the psfgen infrastructure to remove atoms.


CB> Doing that, the psf and pdb files have the same numeration but the output
CB> of the MD simulation does not make sense (I can see atoms collapsing one
CB> upon each other!).
CB> Does anybody can help me?
CB> Thank you in advance for your suggestions,
CB> Caterina

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.