[gmx-users] T->A mutation for a dimer protein
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Jun 23 03:40:20 CEST 2011
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
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