Re: [AMBER] Doubts in MM-PBSA

From: Jason Swails <>
Date: Tue, 22 Mar 2011 18:23:29 -0700

If you got the files straight from VMD (the .dcd file), I have to assume
that is a NAMD trajectory (unless someone else knows better than I do).
According to the AmberTools manual, ptraj can handle CHARMM .dcd files. I'm
not sure if it can handle namd .dcd trajectories -- you'll actually have to
try that out (see the manual and tutorial for learning how to use ptraj).
If ptraj will read .dcd files, then you can use that trajectory with (see for
instructions on how to use and install You should just be able
to use your .dcd file as a normal trajectory in that program. Note that you
will have to create an Amber topology file for your complex, receptor, and
ligand systems (per the instructions in the tutorial above). Please take
time to go through the tutorials carefully if you haven't used any of these
softwares before.

If you do not have Amber, and only AmberTools, then you will have to wait
until AmberTools 1.5 comes out in a few weeks in order to get a copy of that works with AmberTools.

Hope this helps,

On Tue, Mar 22, 2011 at 6:01 PM, vani panguluri <>wrote:

> Actually I am talking about NAMD simulation for performing that simulation
> I
> already used the antechamber forcefield I got the output files such as
> apo.namd, apo.out,apo.dcd, apo.xst like that but I can't able to use the
> MMPBSA TO GET the overall free binding energy. But while I am trying to use
> MMPBSA it was generating the errors. I want to know how can I use that with
> those output files actually I followed that tutorial but it was generating
> some error.
> Regards,
> Vani
> On Mar 22, 2011 6:05 PM, "Jason Swails" <> wrote:
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Tue Mar 22 2011 - 18:30:03 PDT
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