Hydroxamates are also a bit tricky chemically; their chemistry is different than carboxylates or amides, so parameters for the ASP or ASN side chains are unlikely to work. There are also some really old papers from Gilchrist & Jencks on alpha-effect nucleophiles that are good examples of why hydroxylamine can't be thought of as a simple amine.
Therefore, I would suggest a complete parametrization (measuring things like the force constants for stretching the N-O bond, torsion about it, and so on) rather than just getting partial charges. It would seem likely to give better results. cheers, nr On 11/30/06 7:00 AM, "Florian Haberl" <[EMAIL PROTECTED]> wrote: > hi, > > > > On Thursday 30 November 2006 13:01, 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 > >> > >> 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. > > > > A more practical not theoretical idea: > > Use antechamber from Amber suite, it is a nice tool for parametrising unknown > > small molecules (http://amber.scripps.edu/antechamber/antechamber.html). > > > > In the Amber9 handbook (page 74 around) i is described how to use it and i > > think there is a tutorial on the AMBER site around. Fitting of charges will > > be calculated with gaussian or other ab initio suits. > > > > After preparing such a file you can load it in Leap (similar to pdb2gmx) and > > you can complete your input, top and coordinate file will be written, both > > can be transfered to gromacs inputs and after calculation you can use all > > gromacs tools for analysis. > > > > Of course check the in- and output of antechamber, especially atomtypes! > > > >> > >> I also pasted available atom types for Nitrogen in AMBER99 force field. > >> > >> amber99_34 14.01000 ; N sp2 nitrogen in amide groups > >> amber99_35 14.01000 ; NA sp2 N in 5 memb.ring w/H atom > >> (HIS) > >> amber99_36 14.01000 ; NB sp2 N in 5 memb.ring w/LP > >> (HIS,ADE,GUA) > >> amber99_37 14.01000 ; NC sp2 N in 6 memb.ring w/LP > >> (ADE,GUA) > >> amber99_38 14.01000 ; N2 sp2 N in amino groups > >> amber99_39 14.01000 ; N3 sp3 N for charged amino groups > >> (Lys, etc) > >> amber99_40 14.01000 ; N* sp2 N > >> > >> > >> > >> With thanks! > >> B.Nataraj > >> -- > >> raja > >> [EMAIL PROTECTED] > > > > Greetings, > > > > Florian > > _______________________________________________ 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
