From: PAUL NEWMAN (paulclizana_at_gmail.com)
Date: Wed Jun 15 2011 - 00:25:46 CDT

Dear VMD Users

Sorry I just realize that in my last email there is a typo.
I have a problem when building my psf file. The water is forming bonds
between hydrogens. In other words, what I did is that I mutated some animo
acids in my protein (from an equilibrated simulation: protein + water +
ions) and separated the protein from the water and ions in different pdb,
since mutator does not support disulfide patch for proteins. I combine them
using the following script (my pdbs and generating the new psf files) and I
found that the hydrogens in the water are forming bonds between them. I also
checked that in the original psf files there are less bond that in the new
one. I believe I am doing something wrong. Can anyone give me a hand? Thanks

##############################
package require psfgen
topology top_all27_prot_lipid.inp

alias residue HOH TIP3

segment A { pdb protein.pdb }
segment ION { pdb ions.pdb }
segment SOLV { pdb water.pdb}

patch DISU A:19 A:117
patch DISU A:90 A:109

coordpdb protein.pdb A
coordpdb ions.pdb ION
coordpdb water.pdb SOLV

guesscoord

writepsf new.psf
writepdb new.pdb

##############################