Re: fatal error running namd

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Nov 15 2004 - 10:52:34 CST

Hello,

It is possible that order of the water atoms is reversed from what is
expected in the charmm parameter file. Here the water molecule is
described as OT HT HT.

If this is the problem you have two choices, rerun the psfgen script and
correct the order of atoms in each water molecule or just add a new angle
term to the parameter file.

I would try the first for sanity's sake.
regards
Brian

On Mon, 15 Nov 2004, Enrico Piccinini wrote:

> Hi all,
> i'm new using NAMD...
> I have converted a file from Gromacs topology to NAMD and it seemd to
> work properly, but when i run namd2 i always obtain the following fatal
> error:
>
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
>
> I use the last Charmm force field as downloaded from charmm website
> without editing it at all. When i check my topology everything seem ok
> if compared with tutorial examples. Can anyone help me to fix this
> problem?
>
> Enrico
>

*****************************************************************
**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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