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

From: Jason Swails <>
Date: Thu, 18 Sep 2014 08:59:09 -0400

On Thu, 2014-09-18 at 15:15 +0300, Thomas Evangelidis wrote:
> >
> > 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.

Can you make a similar argument about cancellation of errors with
regards to not having periodic images of the membrane?

I believe you are in uncharted waters here with MM/PBSA and MM/GBSA
analyses, so you will likely have to try and answer most of these
questions by trying stuff out.

Good luck!

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 18 2014 - 06:00:05 PDT
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