[AMBER] Calculate MMGBSA keeping water in binding site

From: Rosellen, Martin <martin.rosellen.16.ucl.ac.uk>
Date: Fri, 4 Oct 2019 13:27:27 +0000

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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Received on Fri Oct 04 2019 - 06:30:02 PDT
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