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

SAKO MIRZAIE sako.biochem at gmail.com
Wed Mar 30 20:28:49 CEST 2016

you can use of swisspdbviewer, discovery studio or any other softer to
do mutation of pdb file. then do MD simulation as a separate protein.

On 3/30/16, Tushar Ranjan Moharana <tusharranjanmoharana at gmail.com> wrote:
> 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
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sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj, Iran





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