Re: psgfen patch

From: Peter Freddolino (
Date: Mon Jun 09 2008 - 23:09:06 CDT

Hi Jade,
you may want to have a look at the new extrabonds feature
( if
you really must constrain this particular water to one of its initial

The H-H bonds are a relic from charmm, which requires that bond to
properly set up rigid water geometries (it is ignored in namd). If it
bothers you, you can edit your topology file to remove it by getting rid
of the "H1 H2" portion of the bond line in the definition of TIP3 water.


Hatley, Jade M wrote:
> 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
> guesscoord
> segment 1A1H {
> pdb output/heme.pdb
> }
> coordpdb output/heme.pdb 1A1H
> guesscoord
> alias residue HOH TIP3
> alias atom HOH O OH2
> segment 1A1W {
> auto none
> pdb output/water.pdb
> }
> coordpdb output/water.pdb 1A1W
> guesscoord
> #patch NTER 1A1P:1
> #patch CTER 1A1P:476
> patch HEML 1A1P:426 1A1H:482
> guesscoord
> 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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