Dear GROMACS Users. Just out of curiosity, i would like to pose a general question here ( i didn't have an idea of any other suitable forum ). My protein active site has a GDP which is coordinated to a Mg ion. The Mg ion itself coordinates two water molecules and is held in position via non-bonded interactions from two active site residues. For such a system, I could do two things:
1. Do the charge calculation for GDP only and assume the charges of other active site constituents to be taken from the FF parameter library. 2. As suggested by a a person I know, I can do the charge calculation of the whole system including the Mg ion, water molecules and the residues. The explanation was that since GDP is in coordination to Mg ion, the effective charges would be different than on a GDP alone. Can anyone explain which one of the above is a correct approach and why ? I somehow was not convinced by my co-workers explanation simply considering the fact that for each of the amino acids in a protein the charges and parameters are taken from the FF library. Going by the given explanation, one should then resort to a charge calculation for the whole protein system. Thanks in advance With Regards Abhishek Acharya -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
