The author of such work published partial charges, but nothing about other parameters. The force-fields used are gromos43A1 and CHARMM22. The GROMACS standard distribution contains nothing about iron sulphur cluster.
Thank you 2011/10/6 Mark Abraham <[email protected]> > On 6/10/2011 11:24 PM, francesco oteri wrote: > >> Dear gromacs users, >> >> I've to simulate a protein with an 4Fe-4S and a 3Fe-4S iron sulphur >> cluster. >> Lot of approaches are present in literature. There are a lot of papaers >> suggesting partial charges >> but very few suggestions regarding bonded and not bonded parameters. >> > > All such work should describe a source for such parameters, if they are not > in the standard force field. > > > So i am wondering if any member of this mailing list can send me a link, a >> file or something advice can be useful to >> obtain the topology of a protein with the iron sulphur clusters. >> It is worth noting that I am not interested in electronic properties so >> also advice using restraint are ok for me. >> > > The authors of such work would be a good place to ask. > Mark > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Cordiali saluti, Dr.Oteri Francesco
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