From: Shubhra Ghosh Dastidar (sgducd_at_gmail.com)
Date: Wed Oct 31 2012 - 21:55:49 CDT
I am using the Version 2.9 (2012-04-30)
,Linux-x86_64-multicore-CUDA<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1252>(NVIDIA
CUDA acceleration) to run on a workstation with multicore and
GPU-tesla.
I am using charmm force field to construct a protein-ligand system to run
with namd.
It looks like the NAMD is not supporting 6 character name of the ligand
atom type which is not standard in charmm parameter and giving the
following error for the VDW:
"FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG2R", where CG2R is
an atom of the ligand (small molecule) and the actual atom name is CG2RG1
(i.e. 6 character).
First I discussed in charmm forum and they are says latest NAMD should
support 6 character atom name. So Please give suggestions....should I use
the "Version Nightly Build (2012-10-31) Platforms"?
The relevant portion of the NAMD config file is the following:
---- paratypecharmm on mergeCrossterms yes parameters toppar/par_all22_prot.prm parameters toppar/par_all27_na.prm parameters toppar/par_all36_carb.prm parameters toppar/par_all36_lipid.prm parameters toppar/par_all36_cgenff-no_mass.prm parameters toppar/par_all36_cgenff.prm parameters ligand/ligand.prm --- -- Sincerely, S Ghosh Dastidar
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