water is forming bonds between oxigens

From: PAUL NEWMAN (paulclizana_at_gmail.com)
Date: Tue Jun 14 2011 - 16:36:33 CDT

Dear NAMD Users

I have a problem when building my psf file. The water is forming bonds
between oxigens. 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 followinf script (my pdb with the new generated psf file) and I
found that the oxigens in the water are forming bonds. I checked that in the
origial psf files there are less bond that in the new one. I believe I am
doing something wrong. Can anyone give me a hand?

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

##################################################33

-- 
Cheers,
Paul

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