psgfen patch

From: Hatley, Jade M (
Date: Mon Jun 09 2008 - 12:05:15 CDT

Can someone help with a psfgen script? I have a single water molecule as a segment in my pdb, and I want to patch it as an H-bond to a residue in the protein segment in the psf. As it is now, there is nothing holding the water in place, and it moves considerablely during downstream NAMD simulations. If it cannot be done here can it be done in the NAMD script?
Also, the psf file generated bonds the water incorrectly (3 bonds, O-H, O-H and H-H bonds?!?!)
Any suggestions are appreciated, thanks!

The psfgen script as I have it:

topology top_all22_prot_heme5.inp
alias atom ILE CD1 CD
alias residue HIS HSD
alias residue HEM HEME
segment 1A1P {
 pdb output/prot.pdb
coordpdb output/prot.pdb 1A1P
segment 1A1H {
 pdb output/heme.pdb
coordpdb output/heme.pdb 1A1H
alias residue HOH TIP3
alias atom HOH O OH2
segment 1A1W {
 auto none
 pdb output/water.pdb
coordpdb output/water.pdb 1A1W
#patch NTER 1A1P:1
#patch CTER 1A1P:476
patch HEML 1A1P:426 1A1H:482
writepsf output/<file>.psf
writepdb output/<file>.pdb

Jade M. Hatley, B.S.
Graduate Student
Biochemistry and Molecular Biology
University of Texas-Houston Health Science Center
MSB 3.316

(tel) 713-500-6126
(fax) 713-500-0652

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