From: Vidhya Sankar (vidhyasankar7928_at_yahoo.com)
Date: Wed Oct 09 2013 - 10:57:58 CDT
Dear Namd Users When try to run the simulation it shows the following error
Info: SKIPPING rtf SECTION IN STREAM FILE
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC
Fatal error on PE 0> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC
I Have used the Latest Charmm36 Parameters for Both my POPC lipid and Cyclic Peptide
When I construct The Topology Using Charmm 36 for my in VMD it shows as follows
ERROR! FAILED TO RECOGNIZE 36
duplicate type key H
duplicate type key HC
duplicate type key HA
duplicate type key HP
duplicate type key HR1
duplicate type key HR2
duplicate type key HR3
duplicate type key HS
duplicate type key HE1
duplicate residue key ALA will be ignored
duplicate residue key ARG will be ignored
duplicate residue key ASN will be ignored
duplicate residue key ASP will be ignored
duplicate residue key CYS will be ignored
duplicate residue key GLN will be ignored
duplicate residue key GLU will be ignored
duplicate residue key GLY will be ignored
Warning: poorly guessed coordinates for 24 atoms (6 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 ARG:1 P1
Warning: poorly guessed coordinate for atom HT2 ARG:1 P1
Warning: poorly guessed coordinate for atom HT3 ARG:1 P1
Warning: poorly guessed coordinate for atom HB VAL:2 P1
Warning: poorly guessed coordinate for atom HB THR:4 P1
Warning: poorly guessed coordinate for atom HA PRO:13 P1
Warning: poorly guessed coordinate for atom OT1 PRO:14 P1
Warning: poorly guessed coordinate for atom OT2 PRO:14 P1
How to Solve the Error
Thanks In ADVANCE
With Regards
S.Vidhyasankar
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