[gmx-users] AMBER atom type for Hydroxamate moeity

[raja]

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"
<ncrockwell at ucdavis.edu> 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"
> <Florian.Haberl at chemie.uni-erlangen.de> 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
> > 
> >>   raja_28 at fastmail.us
> > 
> > 
> > 
> > Greetings,
> > 
> > 
> > 
> > Florian
> > 
> > 
> 
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-- 
  raja
  raja_28 at fastmail.us

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