RE: Lithium

From: Scott, Greg (grscott_at_davidson.edu)
Date: Wed Apr 28 2004 - 23:30:08 CDT

It was pointed out to me that I typed in the wrong file. I am, in fact,
using the par_all22_prot.inp file, not the topology file.

Thanks,
Greg

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
Behalf Of Scott, Greg
Sent: Wednesday, April 28, 2004 11:04 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Lithium

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

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