Hi nr, Thanks for your mail. Yea, I am looking for parameters like you mentioned than partial charges.
B.Nataraj On Thu, 30 Nov 2006 09:40:03 -0800, "Nathan C. Rockwell" <[EMAIL PROTECTED]> said: > 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 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow _______________________________________________ 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
