Re: error in starting the minimization

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Nov 12 2003 - 18:11:42 CST

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
>
>

-- 
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**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
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