Re: Lithium

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Apr 28 2004 - 22:59:38 CDT

Hi Greg,

You are using the wrong file for NAMD. The top...inp file is used by
psfgen and charm to create topology files (psf files).

NAMD needs the parameter set in the format of the par_all27prot_XXX.inp
file. Get a copy of that file and then add your potential parameters to
it.

Regards
Brian

On Wed, 28 Apr 2004, Scott, Greg wrote:

> I am new to NAMD and am trying to use it for a simple, non-protein system. Basically, I'm looking at the solvation of lithium and have determined an inner solvation sphere through ab initio computations and want to solvate that further and run MD. I have two problems:
>
> 1) Building the psf file. I couldn't get psfgen to work, but using my pdb file, I used VEGA to create a psf file and hacked around at it until I made it look like I think it should after having read the documentation. Perhaps I have done something wrong here, perhaps not.
>
> 2) A parameter for lithium. I have potential parameters for lithium and tried to add them to the top_all22_prot.inp (which I have renamed lith.param) file using the exact same format as is used for calcium in the non-bonded interactions section.
>
> When I try to run a simulation, I get the following:
>
> FATAL ERROR: UNKNOWN PARAMETER IN XPLOR PARAMETER FILE lith.param
> LINE=**>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<<<*
> Fatal error on PE 0> FATAL ERROR: UNKNOWN PARAMETER IN XPLOR PARAMETER FILE lith.param
> LINE=**>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<<<*
>
> I would appreciate any insight on the matter.
>
> Thank you,
> Greg Scott
>
>

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