Re: [AMBER] Doubts in MM-PBSA

From: Bill Miller III <>
Date: Wed, 23 Mar 2011 09:57:05 -0400

Have you tried reading your trajectory into the ptraj module of AmberTools
to make sure Amber can successfully read it? If ptraj cannot read the NAMD
trajectory, will not be very helpful for you.


On Wed, Mar 23, 2011 at 12:44 AM, vani panguluri <>wrote:

> 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
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/bin
> =>> 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.
> Regards,
> Vani
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Wed Mar 23 2011 - 07:00:06 PDT
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