Re: BOND CP2 - CT2 IN PARAMETER FILES

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Oct 29 2004 - 11:32:18 CDT

hello

You need to find out which bond this is in your system. Do you have a
ligand or special residue that may not be fully described in the parameter
file?

Look in the parameter file for the carbon atoms that are assigned to CP2
and CT2. There are brief notes describing why a carbon would be given
this classification. This should lead you to deciding if a new parameter
is really needed and not that psfgen guessed incorrectly from the info it
was given.

In the future keep this type of email on the namd list, most people who
can help you are already here at namd-l

Regards
Brian

On Thu, 28 Oct 2004, bora erdemli wrote:

> Hi all;
>
> My NAMD run gave me the followig error, as obviously
> be seen that I need a parameter file or I should find
> the parameter of the CP2 - CT2 bond. Is there anyone
> who can help me about it?
>
> sincerely yours
>
>
> ------------- Processor 0 Exiting: Called CmiAbort
> ------------
> Reason: FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR
> BOND CP2 - CT2 IN PARAMETER FILES
>
> req_handle_abort called
> Fatal error on PE 0> FATAL ERROR: CAN'T FIND BOND
> PARAMETERS FOR BOND CP2 - CT2 IN PARAMETER FILES
>
>
> =====
> Sabri Bora Erdemli
> Koc University
> Computational Science and Engineering
> Research and Teaching Asistant
> Koc Universitesi pk.218 34550
> sariyer Istanbul/TURKEY
> tel no: 02123381736
> 05326512523
>
>
>
>
>
>
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*****************************************************************
**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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