From: Amit Paliwal (paliwal_at_jhu.edu)
Date: Tue Mar 30 2004 - 08:45:01 CST
Hi,
I think the problem is that for over 10000 residues you have to divide water
into separate segments otherwise psfgen complains.
thanks,
Amit.
Brian Bennion wrote:
> Hi Amit,
>
> There is no specific max number in psfgen for atoms. What is happening is
> that you are not renaming your segments, most likely.
>
> I have had the same behaviour with my own water boxes. Make sure the
> segment id gets incremented or changeds for each box you place.
>
> for hints own how to do this look at the solvate plugin in vmd
> regards
>
> Brian
>
> On Tue, 30 Mar 2004, Amit Paliwal wrote:
>
> > Hi,
> > I was attempting to make a bigger water box by just translating a
> > smaller one around and get this error
> > while making a psf file:
> > ERROR: failed on residue TIP3 from pdb file
> > duplicate residue key 3700
> > .....
> > I get this for some 3000 residues out of 13000 water residues....
> > Is this a problem related to the max number of water residues that
> > psfgen can handle.
> > -Amit.
> >
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
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