Hi Jason,
Actually what i had done is
1)i want to do MD simulation using NAMD in VMD for protein ligand complex
while doing this i got the PSF file without ligand information so i had
applied antechamber for this .
2)after applying the antechamber i got the coordinate file and prmtop file
and i used them for the NAMD simulation
3)I want to find the binding energy from the output of the NAMD . so one of
my friend told me to use MMPBSA for that,but while doing this i am getting
error like
mm_pbsa.pl (apo1.namd)what was the output file i need give , even i had
tried using different output files that are obtained from namd
=>> Init data
Presuming executables of amber suite to be in
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/bin
=>> Reading input parameters
At-entry must be first
For details see:
http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
I had those MMPBSA.py and MM-PBSA.pl but same error msg i am getting
Could you please help me.
Regards,
Vani
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Received on Tue Mar 22 2011 - 22:00:02 PDT
