[gmx-users] T->A mutation for a dimer protein

[Mark Abraham]

On 23/06/2011 9:48 AM, yaolisha at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110623/ed0b9ef0/attachment.html>