From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Jan 28 2004 - 14:27:50 CST
There may be a bug in psfgen's dihedral generation algorithm, or it's
being confused by duplicate bonds in the topology. I'd need to see the
topology file to understand what's happening.
-Jim
On Wed, 28 Jan 2004, Brian Bennion wrote:
> Psfgen indeed places a repeated dihedral. but I didn't think this was a
> problem initially. Now I am not so sure.
>
> The are three other dihedrals that are repeated in the psf file generated
> by psfgen. ie CA CA CA HP and HP CA CA CA.
>
> Maybe my topology file is causing problems???
>
> Brian
>
>
> On Wed, 28 Jan 2004, Jim Phillips wrote:
>
> > Hi,
> >
> > Looking at the code myself, the only way you should see this error is if
> > you have a repeated dihedral (i.e., same atom numbers) listed in the
> > structure (psf) file. This might be because of a repeated dihedral in the
> > topology file used to generate the structure. Unfortunately the actual
> > atom numbers are not passed to the code that generates this error message.
> > In any case, there are only a small number of atoms to examine in the psf
> > file to check this. Let us know what you find.
> >
> > -Jim
> >
> >
> > On Tue, 27 Jan 2004, Brian Bennion wrote:
> >
> > >
> > > Hello,
> > >
> > > After looking through the code I think I know what is going
> > > on.
> > >
> > > First, I declare my parameter type as charmm format. So
> > > then namd assumes that psf file will only contain torsions that are
> > > unique, within 1 atom.
> > >
> > > Since my ligand has two benzyl groups with the Carbons
> > > assigned the CA type, namd reads the second benzyl group and thinks that
> > > it is adding multiplicity and dies because it isn't in XPLOR mode.
> > >
> > > This, I think, is a bug in NAMD. NAMD needs another check to
> > > show that the second group of CA CA CA CA is unique but doesn't represent
> > > a new torsion parameter. It should use the one already loaded in.
> > >
> > > *****************************************************************
> > > **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 **
> > > **7000 East Avenue phone: (925) 422-5722 **
> > > **Livermore, CA 94550 fax: (925) 424-6605 **
> > > *****************************************************************
> > >
> >
>
> *****************************************************************
> **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 **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:23 CST