Hi, Andrzej,
Please try BUILD_METHOD = 'INTERNAL_COORDINATES', wherever BUILD_METHOD =
'3D_INTERPOLATION' occurs in the script(s). If this does not help, please
send me a sample problem.
Best, Andrej
>
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> Dear Andrej,
>
> I have again ( or additional) problems with MODELLER4.
> I have added all H to short peptide from PBD using 'all_hydrogen.top' script
> from examples directory but result is somehow strange. Some H's are 2.5A away
> but some others only 0.5A from respective root atoms. It could be that it is problem
> with my installation of MODELLER therefore I do not expect that you will work
> on this (unless it is already recognized, general problem). However I will appreciate
> some hints.
> - What is logistic for adding hydrogens to heavy atoms? Formaly it is only
> different library which I am using (top.lib instead of top_heav.lib) but what
> happens in the program?
> - What is the name of subroutine where H atom positions are calculated?
> I think that something is going wrong in this subroutine.
> Of course, if you want, I will inform you about results of my investigations.
>
> Kind regards,
> Andrzej
>
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> n: Sawaryn;Andrzej
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> title: Dr.
> tel;work: +49-451-5004203
> tel;fax: +49-451-5004214
> tel;home: Do not ditsurb me at home!
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--
--
Andrej Sali, Assistant Professor
The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540
e-mail ; http://salilab.org