From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Jun 15 2011 - 01:05:35 CDT
Hi Paul,
sounds like the TIP3P watermodel which has a bond between the hydrogens to
make it more stable and save computing time. Many people use this water
residue because it's cheaper to calculate and most people aren't interested
in realistic moving within a water molecule in forcefield.
Best regards.
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von PAUL NEWMAN
Gesendet: Dienstag, 14. Juni 2011 23:37
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: water is forming bonds between oxigens
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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