From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Jan 28 2004 - 15:32:35 CST
So the problem was actually in my topology file, which was then confusing
the heck out of psfgen and NAMD.
Brian
On Wed, 28 Jan 2004, Jim Phillips wrote:
>
> I think the problem is that C60 C62 appears as both BOND and DOUBLE.
>
> If this fixes things, please post a followup to NAMD-L.
>
> Thanks.
>
> -Jim
>
>
> On Wed, 28 Jan 2004, Brian Bennion wrote:
>
> > oops sorry,
> >
> > RESI PTI
> >
> > The psfgen script I used is also attached.
> > Brian
> >
> >
> >
> > On Wed, 28 Jan 2004, Jim Phillips wrote:
> >
> > >
> > > So, what residue should I be looking at here?
> > >
> > > -Jim
> > >
> > > On Wed, 28 Jan 2004, Brian Bennion wrote:
> > >
> > > >
> > > > Here is the topology file.
> > > > I was able to pick out the atom numbers from Molecule.C.
> > > > I deleted the extra torsion entries from the psf file, but that lead to
> > > > new problem with the angle energies being -999999.9 depending on the size
> > > > of the periodic cell.
> > > >
> > > > Brian
> > > >
> > > >
> > > >
> > > > On Wed, 28 Jan 2004, Jim Phillips wrote:
> > > >
> > > > >
> > > > > 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 **
> > > > > > *****************************************************************
> > > > > >
> > > > >
> > > >
> > > > *****************************************************************
> > > > **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 **
> > *****************************************************************
> >
>
*****************************************************************
**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 **
*****************************************************************
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