Re: AMBER: How to calculate the mmpbsa for explicit MD ?

From: Thomas Steinbrecher <>
Date: Mon, 12 Jun 2006 09:58:33 -0700 (PDT)

Hi Jitrayut,

> I am new for mmpbsa and I look at the mmpbsa tutorial which is an implicit
> md. For explicit MD, I found the error say that "NATOM mismatch between
> topology and coordinate" in sander output. I think that maybe somethings
> wrong in step of generating topology of COM,LIG and REC. So, I want any
> suggestions about generating topology file for explicit MD.

MM-PBSA always contains an implicit solvent step in the calculation of
solvation free energies, so I assume you mean running an MM-PBSA
calculation on trajectories generated from a simulation with explicit
waters. Therefore you need to prepare parameter files for your receptor,
ligand and complex without water molecules. The MM-PBSA script strips
waters and counterions from your trajectories so you need those parameter
files to run on your snapshots.

I would assume the error comes from starting a sander calculation on a
'naked' receptor with the parameter file of the solvated receptor.


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Received on Wed Jun 14 2006 - 06:07:11 PDT
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