Re: error in starting the minimization

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Nov 14 2003 - 14:41:35 CST

Hi,

This is a good lesson. The GLY residue definition includes the statement
"PATCHING FIRS GLYP", which tells psfgen to *automatically* apply this
patch if GLY is first in a segment, overriding the file-default NTER.

Therefore, you should avoid explicitly listing first/last patches for
protein segments unless you need special terminal groups.

-Jim

On Wed, 12 Nov 2003, Ruxandra Dima wrote:

> Hello Brian,
>
> I think I know what the problem is. My first residue is a GLY. I made the
> mistake of assigning NTER for capping it and I think that this is why it
> is complaining (I deleted the GLY, re-did all the settings and now
> minimization goes ahead with no problems). I searched the topology file
> for charmm27 and I found something called GLYP which looks like the
> equivalent of NTER for GLY at N-terminus.
>
> Thank you,
>
> Ruxandra
>
> On Wed, 12 Nov 2003, Brian Bennion wrote:
>
> > Hello Ruxandra,
> >
> > Lets take a step back here from namd...
> >
> > Somehow your psfgen file is describing a carbon incorrectly. CT1
> > carbon atoms only have one hydrogen bond to them so naturally you get the
> > fatal error from NAMD because the parameter doesn't exist in charm27
> > libraries.
> >
> > So first find out where this carbon atom is and if it has two hydrogens
> > bound.
> >
> > it would be nice if a psf and pdb file were included as attachments (as
> > long as they are not huge).
> >
> > Brian
> >
> >
> > On Wed, 12 Nov 2003, Ruxandra Dima wrote:
> >
> > > Hello,
> > >
> > > I am trying to minimize a system made out of a protein structure taken
> > > from the PDB and water (added using solvate 1.2). Upon starting the
> > > minimization process with the protein backbone frozen, I get the error
> > > message:
> > >
> > > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
> > >
> > > Could anyone help me understand what it means and how I can avoid it?
> > >
> > > (I checked the parameter file from charmm27 and there is an entry for
> > > HB CT2 HB, but nothing for HB CT1 HB. If I put some dummy value for
> > > HB CT1 HB, it passes this point but during the minimization it complains
> > > at each step that "Warning: Not all atoms have unique coordinates.")
> > >
> > > Thank you,
> > >
> > > Ruxandra
> > >
> > >
> >
> > --
> > *****************************************************************
> > **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) 422-6605 **
> > *****************************************************************
> >
> >
> >
>

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