Re: minimization problem

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Mar 18 2004 - 18:00:23 CST

Hello Olya,

The bond section of your residue declaration in the topology file is
probably not correct and therefore your psf file has this bond linked in.

Check the psf+pdb file in vmd and look for extraneous bonds...

Regards
Brian

On Thu, 18 Mar 2004, Olya Kravchenko wrote:

> Dear all! I have the following problem:
>
> I'm trying to minimize the structure of part of the molecule that I have
> edited by myself into the topology file (heme A type) and thus edit parameter
> file for missing bonds and angles (measure them in vmd, then write those into
> the parameter file with constants from similar bonds and angles that are
> already in parameter file). I get the following error:
>
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 C CT3
> Aborted
>
> But I don't have such an angle in my structure! The atom types that I assigned
> to my structure seem to be correct. What can I do to resolve this?
>
> Thank you very much in advance!
>
> Olya
>

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