[gmx-users] AMBER atom type for Hydroxamate moeity

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Thu Nov 30 16:00:39 CET 2006


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
> amber99_37        14.01000      ; NC  sp2 N in 6 memb.ring w/LP
> 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
>   raja_28 at fastmail.us



 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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