Hello Joao Thanks for the reply; I am planning to use Amber 99SB-ILDN force field.
I just wanted to know which parameter set is the most suitable for ATP/Mg (in terms of reproducing the right geometry etc) in conjunction with any force field. Best George > Hello George, > > What do you mean by "best"? It really depends on the force-field that you > are using/intend to use. > > Best, > Jo?o > > > On Fri, Apr 26, 2013 at 4:00 PM, George Patargias > <[email protected]>wrote: > >> Hello >> >> Doe anybody know what is the "best" (the most suitable) set of >> parameters >> to use for ATP/Mg+2 ? >> >> I have seen from the literature that people have used mainly either the >> CHARMM27 parameters or the ones in >> >> Meagher KL, Redman LT, Carlson HA (2003) Development of polyphosphate >> parameters for use with the AMBER force field. J Comput Chem 24:1016 >> >> I would appreciate if you can give me any hints on this. >> >> Thanks. >> >> >> Dr. George Patargias >> Postdoctoral Researcher >> Biomedical Research Foundation >> Academy of Athens >> 4, Soranou Ephessiou >> 115 27 >> Athens >> Greece >> >> Office: +302106597568 >> >> -- >> 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 >> > > > > -- > Jo?o M. Damas > PhD Student > Protein Modelling Group > ITQB-UNL, Oeiras, Portugal > Tel:+351-214469613 > -- > 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 > Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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
