From: Albert (mailmd2011_at_gmail.com)
Date: Fri Mar 30 2012 - 02:37:10 CDT
Hello:
I've generated a system containing a ligand within it by CHARMM-GUI.
and I am trying to run step6.1 keeping all parameters unmodified by command:
namd2 +p8 step6.1_eq.inp >log &
but it said from log file:
Info: COORDINATE PDB ../step5_assembly.pdb
Info: STRUCTURE FILE ../step5_assembly.xplor.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS toppar/par_all22_prot.prm
Info: PARAMETERS toppar/par_all27_na.prm
Info: PARAMETERS toppar/par_all36_carb.prm
Info: PARAMETERS toppar/par_all36_lipid.prm
Info: PARAMETERS toppar/par_all36_cgenff.prm
Info: PARAMETERS toppar/toppar_water_ions.str
Info: PARAMETERS toppar/toppar_all36_lipid_cholesterol.str
Info: PARAMETERS toppar/lig.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 1314 BONDS
Info: 3871 ANGLES
Info: 9238 DIHEDRAL
Info: 274 IMPROPER
Info: 6 CROSSTERM
Info: 481 VDW
Info: 6 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG32
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG32
Charm++ fatal error:
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG32
does anybody have any idea how to solve this problem?
THX
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