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 <tusharranjanmohar...@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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- *********************************************** sako mirzaie PhD in biochemistry, science faculty, Islamic azad university of sanandaj, sanandaj, Iran http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie http://scholar.google.com/citations?user=viwZvVAAAAAJ&hl=en http://www.scopus.com/authid/detail.url?authorId=54886431500 http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie https://www.researchgate.net/profile/Sako_Mirzaie/publications/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.