AMBER Archive (2006)

Subject: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ?

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Mon Jun 12 2006 - 13:37:49 CDT


Dear *Thomas Steinbrecher*

Thank you for your kind answer but I am still confused about MM-PBSA script
that you say strips waters and counterions from the trajectorie. Please
explain in more specific details or how I can do with this script.

Best regards

Jitrayut

---------- Forwarded message ----------
From: Thomas Steinbrecher <steinbrt_at_scripps.edu>
Date: 12 .. 2006, 23:58 .
Subject: Re: AMBER: How to calculate the mmpbsa for explicit MD ?
To: amber_at_scripps.edu

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.

Regards,

Thomas
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