Re: MMPBSA-like analysis

From: Hannes Loeffler (
Date: Wed Oct 30 2013 - 08:24:43 CDT

On Wed, 30 Oct 2013 17:55:18 +0530
Revthi Sanker <> wrote:

> Dear Sir,
> Thank you so much for the reply. I had run my MD simulations of the
> protein-receptor complex for 100ns with my script using CHARMM36 in
> NAMD. All that is left to do is to perform the MMPBSA analysis on this
> trajectory. Could you let me know in detail how to go about with this
> analysis? Do you have any tutorial for the same as I am a beginner to
> MD? Kindly provide your valuable suggestions.

Well, I'm afraid I have no detailed instructions and you will have to
make yourself familiar with CHARMM and its scripting facility.
mm-pbsa.inp is a CHARMM script you will need to adapt to your needs.
The script assumes that you have compiled CHARMM with iAPBS support

One final note though: my script assumes a single input trajectory
because I had extracted the complex only coordinates into a single DCD.
Also, take into account the possible pitfalls discussed earlier.

Good luck,

Scanned by iCritical.

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