Dear Chris and Mark,
Thank you both for the response. I did the simulation already and Gromacs
only gives me the total dH/dl. The two mutated sites are more than 20A alway
from each other which makes it safe to assume that the interaction between the
two sites is small. If I can extract dH/dl for each site, I could get a
resonable error estimation of my calculation. Furthermore, if this is reliable
I will do different mutations in two monomers (as long as they are away from
each other) so that I can save my computational time by 50%. I guess this will
involve some code change.
Best,
Lishan
> From: chris.ne...@utoronto.ca
> Subject: [gmx-users] T->A mutation for a dimer protein
> To: gmx-users@gromacs.org
> Message-ID: <20110622210442.mmbm5utlww08k...@webmail.utoronto.ca>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Lishan:
>
> First, it would be great to see some evidence that you have tried to
> do this yourself before posting. Your "I think" makes it a possible
> waste of time for us to suggest a resolution to a problem that may or
> may not exist.
>
> Second, if indeed it is a problem, perhaps you could use two identical
> topologies with different molecule names and treat them separately.
>
> Chris
>
Message: 3
Date: Thu, 23 Jun 2011 11:40:20 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] T->A mutation for a dimer protein
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4e029984.9040...@anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"
On 23/06/2011 9:48 AM, yaoli...@msu.edu wrote:
>
> Hi All,
> I have a protein dimer and I want to calculate a T to A mutation free
> energy change using TI method. Since it is a dimer, it is very
> convenient (and advantageous) to mutate the T in both monomer
> simultaneously. Gromacs will write out dH/dl sum for the two mutations
> together, I think. My question is how can I change Gromacs so than
> dH/dl for T->A mutation in each monomer is written out separately?
>
You can't, because both have contributions from all the interactions. If
your method is sound, i.e. both mutations can take place without
affecting the other (big assumption IMO), surely you can just halve
dH/dl from the combined mutation to get the single-mutation dH/dl?
Mark
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