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

and also this one: http://www3.mpibpc.mpg.de/groups/de_groot/cecam2015/peptide_mutation/ On 3/31/16, SAKO MIRZAIE wrote: > hi > you can do MD simulation and compute free energy of folding, > individually. for detect the folding frame or structure, use have to > regard to

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

hi you can do MD simulation and compute free energy of folding, individually. for detect the folding frame or structure, use have to regard to RMSD. please look at the following webpage: http://www3.mpibpc.mpg.de/groups/de_groot/compbio2/p8/index.html On 3/31/16, Tushar Ranjan Moharana

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

Hi SAKO MIRZAIE, Thanks for your reply. But how can we calculate difference in folding free energy by doing 2 separate simulations? Please clarify (at least give some hints or references). Thanks a lot. "A society with free knowledge is better than a society with free food" -- Tushar Ranjan

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

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 wrote: > Hi Everyone, > > I want to find the change in delta G between a protein and its

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

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