Dear All,
I am simulating a protein in gromacs with amber force field. The protein shows maximum biological activity at pH 5.0 and at pH 7.4 it shows no activity. So whichever biological process I am going to model should be at the biologically active pH . So can anyone suggest me 1) how to get the protonation state of each and every residues present in the protein at that particular pH [i.e. at pH 5.00] ? Should I look into the pKa values of each and every residues from standard table to or is there any software to find the same ? 2) how to get the net charge of the protein at that particular pH ? [ Protein Calculator !! ] Thanks in advance. -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
