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

From: Rosellen, Martin <>
Date: Sat, 5 Oct 2019 13:40:18 +0000

Hi Carlos,

thanks for your comment. I use GB model 2 (Onufriev, Bashford, Case) with mbondi2 radii.


Message: 14
Date: Fri, 4 Oct 2019 09:35:40 -0400
From: Carlos Simmerling <<>>
Subject: Re: [AMBER] Calculate MMGBSA keeping water in binding site
To: AMBER Mailing List <<>>
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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?

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