Re: error in starting the minimization

From: Ruxandra Dima (dimar_at_Glue.umd.edu)
Date: Wed Nov 12 2003 - 18:20:53 CST

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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>
>

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