Reg Lack of Lack of VDW parameters

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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