Nicolas,
With respect to non bonded terms, by default, Modeller relies on distant
restraints and a lower bound repulsive potential (soft sphere) i.e does not see
charges. Consequently it will try to retin as much of the template residue
conformation as possible.
You can try alternative solutions to see alterantive conformations. E.g. if you
concerned about charges, switch on electrostatic potential by including in your
top file:
SET DYNAMIC_COULOMB = on
another trick would be to remove the template residue. In that case modeller
will build the new residue without "homology derived" restraints.
Andras
Dr Nicolas Le Novere wrote:
>
> Dear users,
>
> In a model I got with MODELLER, there is a potential hydrogen bond
> between oxygens of a glutamate and an aspartate (or the respective acids).
> However there is supposedly an important electrostatic repulsion.
>
> In the template the aspartate is replaced by a glycine. There is room
> for several of the glutamate conformers. Is it normal that MODELLER
> made the choice to keep the original conformer of the glutamate even
> with the unfavourable electrostatic environment?
>
> Regards,
>
> --
> Dr Nicolas Le Novère http://www-alt.pasteur.fr/~lenov
> Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK
> tel: +44 1223 336623 fax: +44 1223 336676 e-mail:
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras