Hi Liz,
totally agree with Paul :). Making a new ligand within coot
is not the choice of program to use.
I would suggest creating yourself a smiles of you ligand
incl. H-atoms and running corina.
Or you could even draw your mutated ligand in Isis.
Or for the easier have a look at
http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_comp.html
Cheers
Stefan
On Thu, 23 Jun 2011 12:55:06 +0530
Elizabeth Varughese <[log in to unmask]> wrote:
> hi,
>
> I have to mutate 6 membered ring structure, with 2 Natoms
> and 4 C atoms.
> There was no hydrogen atom on the nitrogens. after
> necessary mutations i
> have add a hydrogen atom on one of these N atoms. But due
> to the diff in
> bond lengths H is not adding.
> So i have to slightly change one of the bond lengths to
> make it single bond.
> is there any method to do this with altering or breaking
> the whole rong
> structure.
>
> Mary
> Research Scholar
> SPAP
> M.G.University
> India
Dr Stefan Gerhardt
Albert-Ludwigs-Universität Freiburg
Inst.f.Org.Chem.u.Biochem
Albertstrasse 21
79104 Freiburg
Tel. +49 761 2035970
Fax. +49 761 2036161
|