RE: proper order for par files in namd (solved)

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Fri Apr 24 2015 - 18:21:22 CDT

This order works....

parameters ../toppar/par_all36_prot.prm
parameters ../toppar/par_all36_carb.prm
parameters ../toppar/par_all36_lipid.prm
parameters ../toppar/par_all36_cgenff.prm
parameters smallMolecule.par
parameters ../toppar/toppar_water_ions_namd.str
________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Bennion, Brian [bennion1_at_llnl.gov]
Sent: Friday, April 24, 2015 3:05 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: proper order for par files in namd

hello,

I have been bit by the VdW parameter not found error for running a namd simulation in the par36 force field.

There seems to be a proper order of files so that atom types are correctly noted. What is it????
The following order generates the following errors.

par_all36_prot.prm
par_all36_lipid.prm
par_all36_na.prm
par_all36_carb.prm
par_all36_cgenff.prm
smallCgenFFMolecule.par
toppar_water_ions_namd.str

 FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OCL
 FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2

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