Hi Florian, Thanks for your mail and introducing me the Antechamber site. I am trying out there in that site.
B.Nataraj On Thu, 30 Nov 2006 16:00:39 +0100, "Florian Haberl" <[EMAIL PROTECTED]> said: > 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 > > -- > ------------------------------------------------------------------------------- > Florian Haberl > Computer-Chemie-Centrum > Universitaet Erlangen/ Nuernberg > Naegelsbachstr 25 > D-91052 Erlangen > Telephone: +49(0) − 9131 − 85 26581 > Mailto: florian.haberl AT chemie.uni-erlangen.de > ------------------------------------------------------------------------------- > _______________________________________________ > 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 - Access all of your messages and folders wherever you are _______________________________________________ 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
