Re: [AMBER] Doubts in MM-PBSA

From: vani panguluri <>
Date: Tue, 22 Mar 2011 23:44:52 -0500

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 (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

=>> Reading input parameters
    At-entry must be first
    For details see:

I had those and but same error msg i am getting
Could you please help me.

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Received on Tue Mar 22 2011 - 22:00:02 PDT
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