Re: [AMBER] PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions

From: Thomas Evangelidis <>
Date: Thu, 18 Sep 2014 15:15:42 +0300

> never accounts for PBC. There is only one GB implementation
> that I'm aware of that does (and I don't know how much sense such an
> approach makes).
> You may want to look into the membrane capabilities of PBSA. It's
> relatively new functionality, but it was designed for studies like this
> (it treats the membrane and solvent implicitly by setting up multiple
> dielectric regions).
Thank you. I just had a look. I must define the membrane thickness and the
cylindrical exclusion region at the center of the protein. I have done this
in the past with APBS for individual protein models and I spent a lot of
time for trial, error and visualization until I find the optimum values,
which were still not perfect. I think I could avoid all this if I measure
relative free energies of binding for the ligands I have as I would do for
a water soluble protein. Unless I am missing something, the terms
accounting for solvation and desolvation of the transmembrane part of the
protein with cancel out.

> > And the second query has to do with mpi. I don't have the AMBER14 source
> > yet, so I cannot compile AMBER-MPI version (AMBER12 fails to compile with
> > AmberTools14). So, although serial execution of runs smoothly,
> > when I invoke it with mpirun it runs multiple times the same calculation.
> > Does this have to do with compilation of AMBER14 source?
> You need to invoke with mpirun. is strictly
> serial. The former is built with AmberTools 14 (as long as you build
> AmberTools 14 in parallel).
> Hope this helps,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens

*Physics is the only real science. The rest are just stamp collecting.*
*- Ernest Rutherford*
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Received on Thu Sep 18 2014 - 05:30:03 PDT
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