[gmx-users] AMBER atom type for Hydroxamate moeity

[raja]

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"
<Florian.Haberl at chemie.uni-erlangen.de> 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
> >   raja_28 at fastmail.us
> 
> Greetings,
> 
> Florian
> 
> -- 
> -------------------------------------------------------------------------------
>  Florian Haberl                        
>  Computer-Chemie-Centrum   
>  Universitaet Erlangen/ Nuernberg
>  Naegelsbachstr 25
>  D-91052 Erlangen
>  Telephone:      +49(0) &#8722; 9131 &#8722; 85 26581
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
> -------------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- 
  raja
  raja_28 at fastmail.us

-- 
http://www.fastmail.fm - Access all of your messages and folders
                          wherever you are