VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 15 2011 - 10:38:26 CDT

On Wed, Jun 15, 2011 at 1:25 AM, PAUL NEWMAN <paulclizana_at_gmail.com> wrote:
> 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

bonds between the hydrogens are normal for CHARMM (and Amber).
to keep a water molecule rigid, you can either use two bond constraints
and an angle or use three bonds. NAMD will ignore it. no worries.

axel.

> 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
>
> ##############################
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.