Thanks Mark for your reply. And sorry about missing one hydrogen in my drawn topology...
B.Nataraj On Thu, 30 Nov 2006 23:12:10 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear gmxions, > > I am writing a topology for a ligand using AMBER99 force field > > convention. The ligand contains the hydroxamate group, for your quick > > reference I have drawn it below > > > > O > > HO || > > \ / \ > > N > > Your N has an unsatisfied valence... what's missing? (Don't bother to > tell me, it doesn't matter) > > > Please let me know which atoms type in amber can be used for these > > atoms.... Especially the Nitrogen atom in this group. Since I am using > > carbonyl group and hydroxyl group atoms types for oxygen (But I am not > > sure of its validity). Please help me to chose appropriate atoms type. > > Probably, none of them. Force fields are not magic numbers that can be > applied to all possible "types" of atoms. They are constructs designed > to be reliably applicable to fairly narrow sets of atom types under the > range of conditions they were parametrized with (also normally narrow). > You will see this when you read the paper that describes the development > process of this force field. Notwithstanding, people routinely abuse > them with gay abandon, probably on the bad advice of others, or their > own experience of the fairly good transferability of quantum-chemical > methods. > > Your only vaguely reliable course is to find a set of experimental data > consistent with those used for the development of the force field, work > out what new values you need to derive and to follow a process to > optimize those values to reproduce the experimental data. This process > is not for the inexperienced, or for the faint of heart. > > Otherwise, you'll have the usual expensive random number generator. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - mmm... Fastmail... _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
