[AMBER] TI for mutation of charged residues

From: Hosein Geraili Daronkola <geraili.hsn.gmail.com>
Date: Mon, 29 Jul 2019 09:17:05 +0200

Hi all,

I am trying to use Ti on pmemd to mutate Aspartate to Asparagine on a
protein. The problem is that this mutation ends in a charged state because
I add counterion in the beginning and start from a neutral state. Is there
an analytical way to remove this effect of ending in a charged state, one
extra potassium at the end??
I tried to mutate both Asp and potassium together to Asn, but the problem
is that they should stay far away to not have a cooperative effect, so I
could subtract the solvation free energy of potassium from the combination,
but I cannot increase the box size reasonably enough to get rid of this
cooperative effect between a negatively charged residue, Asp, and
positively charge ion, potassium.

Thanks in advance
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Received on Mon Jul 29 2019 - 00:30:02 PDT
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