Re: [AMBER] Calculate MMGBSA keeping water in binding site

From: Carlos Simmerling <>
Date: Fri, 4 Oct 2019 09:35:40 -0400

GB is notoriously poor at desolvation estimates for Arg. Which gb model and
radii set are you using?

On Fri, Oct 4, 2019, 9:28 AM Rosellen, Martin <>

> Dear Amber Users,
> I am introducing mutations in a binding site between an antibody and a
> protein. The MMGBSA calculations do correlate with experimental data in
> most of the cases. In one case where I mutate an arginine to an alanine
> MMGBSA overestimates the loss in binding energy. Water is coming in at the
> location of the mutation. I would like to do MMGBSA calculations including
> the water at this location. I use 150 frames in the calculations.
> So far, I calculated the contacts of this residue to the solvent by:
> nativecontacts :42 :WAT writecontacts solvent_contacts.dat resout
> solvent_contacts_res.dat out solvent_contacts_out.dat includesolvent
> contactpdb solvent_contacts.pdb
> In the output files I only found information about 'How many water
> contacts there are in one frame' or 'What fraction of time a specific water
> contact can be observed'. What I am missing is the information 'What
> contacts are in frame 1,2,3,... etc.'. I thought about a workaround,
> loading one frame at a time and calculate nativecontacts but maybe you know
> an easier way?
> cheers
> Martin
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Received on Fri Oct 04 2019 - 07:00:02 PDT
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