[gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

[Tushar Ranjan Moharana]

Hi Everyone,

I want to find the change in delta G between a protein and its mutant (with
two amino acid mutation). I know for this I have to use "dual topology
approach" as mentioned in the manual section 5.7.4. I still couldn't get
how to create such a topology. Is there any direct way (like pdb2gmx or any
other program). If not then can any body explain me the way to do so(I can
write perl script if necessary).

Thanks a lot for your time and effort.

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB