Re: [AMBER] Problem when calculating MMPBSA

From: Jason Swails <>
Date: Tue, 21 Jan 2014 23:04:35 -0500

On Tue, Jan 21, 2014 at 9:31 PM, dongying0512 <> wrote:

> Hi Jason,
> Thank you for your help. I indeed did it in a wrong way.
> I still have some problems and maybe because I use 'chamber' in a wrong
> way. I convert the pdb and psf files to prmtop in the following way.
> I know when calculating the MMPBSA I must have four prmtop files, for the
> solvated system, the complex, the receptor and the ligand. I had the pdb
> and psf files for the solvated system. And I saved the pdb and psf files
> for the complex, receptor and ligand from the solvated system in VMD. Then
> I converted the files to prmtop files using chamber. But when run the
>, it seemed that the prmtop files of the solvated system, the
> complex, the receptor and the ligand were not compatible.
> What is the right way to do that? Please help me.

You need to create them to be compatible in the first place. There is no
automated way to do this when you use chamber, as does not
work with chamber-created topologies.

Make sure that the complex topology file is the same as the solvated
topology file without any water or ions (unless you plan to explicitly keep
some ions around, in which case you need to adjust strip_mask in the input file). Likewise, the receptor topology file needs to have
every atom in the complex topology file EXCEPT the ligand atoms (and the
ligand topology file must contain ONLY the ligand atoms).

You can look through the prmtop files you generate to check them. Look at
the RESIDUE_LABEL section and make sure the residue sequence is what you
expect it to be. Also make sure that the number of atoms (first number in
the POINTERS section -- see is consistent.
 That is, the complex has the same number of atoms as the sum of the
receptor and ligand. These are just 2 suggestions -- there are certainly
more checks you can do.

In summary, there are many ways that you can get 'incompatible' topology
files, and using chamber increases the number of ways to make a mistake.
 This will likely require some investigation.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 21 2014 - 20:30:02 PST
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