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

From: Carlos Simmerling <>
Date: Thu, 10 Oct 2019 14:06:05 -0400

we have a few papers looking at performance of GB vs explicit water for
salt bridges (see below). I don't recall testing igb=2, but the others tend
to overestimate strength, especially with mbondi2. We recommend mbondi3
along with igb=8, see the Nguyen et al paper below for analysis.

Improved Generalized Born Solvent Model Parameters for Protein Simulations
Nguyen, H., Roe, D. R., Simmerling, C., Journal of Chemical Theory and
Computation, 2013, 9 (4), 2020-2034
DOI: 10.1021/ct3010485
PMCID: PMC4361090

Improving the description of salt bridge strength and geometry in a
Generalized Born model
Shang, Y., Nguyen, H., Wickstrom, L., Okur, A. and Simmerling, C., Journal
of Molecular Graphics and Modelling., 2011, 29, 676-684
DOI: 10.1016/j.jmgm.2010.11.013
PMCID: PMC3390179

Evaluation of salt bridge structure and energetics in peptides using
explicit, implicit and hybrid solvation models
Okur, A., Wickstrom, L. and Simmerling, C.
Journal of Chemical Theory and Computation, 2008, 4 (3), 488-498
DOI: 10.1021/ct7002308

Investigation of salt bridge stability in a Generalized Born solvent model
Geney, R., Layten, M., Gomperts, R., Hornak, V. and Simmerling, C.
Journal of Chemical Theory and Computation, 2006 , 2 (1), 115-127
DOI: 10.1021/ct050183l

On Sat, Oct 5, 2019 at 9:40 AM Rosellen, Martin <> wrote:

> Hi Carlos,
> thanks for your comment. I use GB model 2 (Onufriev, Bashford, Case) with
> mbondi2 radii.
> best
> Martin
> Message: 14
> Date: Fri, 4 Oct 2019 09:35:40 -0400
> From: Carlos Simmerling <<mailto:
> Subject: Re: [AMBER] Calculate MMGBSA keeping water in binding site
> To: AMBER Mailing List <<>>
> Message-ID:
> <
> <
> >>
> Content-Type: text/plain; charset="UTF-8"
> 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 <
> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Thu Oct 10 2019 - 11:30:02 PDT
Custom Search