From: Scott, Greg (grscott_at_davidson.edu)
Date: Wed Apr 28 2004 - 22:04:14 CDT
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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