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Re: All H in MODELER



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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-- 
--
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