From: James Starlight (jmsstarlight_at_gmail.com)
Date: Thu Nov 07 2013 - 01:53:52 CST
Dear namd users!
1) I have some problems with the ussage of NAMD energy plugin for the
system consisted of membrane, protein and ligand. Firstly I've defined in
GUI to calculate potential for "protein" selection providing .par files for
protein lipids and ligand. When I try to do computations I have error
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE NG3P
where this atom correspond to the ligand atom (par have been defined as the
separate par files).
How I could solve it?
2) Also I have a question about values produced in the LOG file. Does it
values in KCal/mol?
For example using tcl script for computation of the <Udih> along trajectory
I ve obtained DIHED: 10022.468879276325 which should correspond to the VERY
tense system. Typically as I know <Udihe> for 400 amino acid protein
protein should be 1500-2000 and extra 1000 contribution from the ~ 150
Does this values corrects?
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