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
