Hello George, You need to use Antechamber, a software provided by the amber developers in a free Amber Tools package. That will produce the right parameters for the Amber force feild.
Cheers Abhishek 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 >> <g...@bioacademy.gr>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 gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> * 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 gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> * 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
