AMBER Archive (2006)

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

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Mon Jun 12 2006 - 14:23:01 CDT

My recollection is that you have to make 3 prmtop files with leap,
manually. That's what the manual means by "The user has to prepare
prmtop files for receptor, ligand, and complex..."

Load your start pdb (remove any crystallographic waters) into leap, use
saveamberparm to create a prmtop for the complex, which is the combined
ligand and receptor.

Edit the start pdb to remove the ligand, load that into a new leap
session, and save that as the receptor prmtop.

Fianlly, create a pdb which has only the few ligand atoms, and use leap
to save that small pdb file as the ligand prmtop.

Chris

jitrayut jitonnom wrote:
> Dear amber users
>
> 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.
>
> Thanks in advance for any suggestions
>
> Best regards
>
> Jitrayut
>
>

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