Re: [AMBER] MMPBSA, ligand sequence

From: Jason Swails <>
Date: Fri, 25 Oct 2013 07:22:32 -0400

On Fri, Oct 25, 2013 at 6:29 AM, maghtar <> wrote:

> Dear AMBER users,
> I am new in AMBER. I have a structure including a protein and chromophores.
> I want to calculate the vibrational modes of the chromophores. I am
> following the AMBER tutorial for the calculation of binding entropy using
> MMPBSA; but I am getting the following error:
> PrmtopError: Couldn't predict mask from topology files!
> Your ligand residues must be sequential in your complex.
> There are likely problems with your topology files if this is not the case.
> Exiting. All files have been retained.
> It seems it is because my ligand is not a protein so the program can not
> guess the residues of the ligand.

The ligand does not have to be a protein for this mask guesser to work.
 The mask guesser works by trying to place the ligand residue sequence
inside the receptor residue sequence and checking to see if it matches the
full bound complex residue sequence. It will not, however, try to break
the ligand into 'pieces' to match the sequence, so if your ligand is not
comprised of residues that appear continuously in the complex (like your
ligand_mask tends to suggest), then the default mask guesser will obviously
not work.

After some search I got to this point
> that I need to use the ligand_mask option but I am still getting the same
> error. This is my input file:
> &general
> endframe=10, keep_files=2,
> ligand_mask=:299:477:498:499:501:502:504:505,

This is not enough. You also need to specify receptor_mask. If you only
specify one mask, will attempt to use the defaults (resulting in
the same error, as you observed). If you are using AmberTools 13, this
should have been printed as a warning, wasn't it?

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 25 2013 - 04:30:02 PDT
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