[gmx-users] AMBER atom type for Hydroxamate moeity

[Nathan C. Rockwell]

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
> 
>