Re: [AMBER] Residue mismatch - Amber11

From: Jason Swails <>
Date: Tue, 10 Apr 2012 23:14:03 -0400

On Tue, Apr 10, 2012 at 5:47 PM, sławek bojarowski <>wrote:

> Hi,
> I've got such as error, while using Amber11's MMPBS:
> "Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> Error: Residue mismatch in your prmtop files! Complex res != Receptor res
> + Ligand res."

This is one of the many checks that does to make sure that your
topology files are compatible with one another. What this check says is
that the number of residues in your complex is not equal to the number of
residues in your receptor + number of residues in your ligand. Indeed, if
you look at your topology files, each system is defined as a single residue.

It also seems like this is the first example I've ever seen in which your
topology files may be consistent, yet the residue numbers do not match up
as expected, which leads me to the question -- how did you make this
topology file? If you are certain that your topology files are correct,
you can comment out the error catch in, but there is a good
reason they are there in the first place.


P.S. The only way I can think of that you actually made these topology
files is that you generated two separate mol2 or OFF library files -- one
with the monomer and one with the dimer, and each of them is defined as a
single residue in that library file. What I suggest doing instead is to
generate all 3 topology files with the monomer library file, so that the
complex is defined as 2 uracil residues.

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Apr 10 2012 - 20:30:03 PDT
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