23 May
2014
23 May
'14
2:31 p.m.
Alexander,
The program Reduce from the Richardson lab ( http://kinemage.biochem.duke.edu/software/reduce.php ) does a good job adding hydrogens to protein structures, and there are many other modeling programs that can perform that step (some listed here: http://kpwu.wordpress.com/2012/02/24/add-protons-hydrogens-to-structure/ ).
Although these programs will not solve your problem if you must *preserve* the locations of hydrogens in the structure you input to Modeller, that requirement is relatively uncommon.
Hope that helps, -J'n
--
Jonathan Sheehan, Ph.D.
Computational Structural Biology
Vanderbilt Univ. Ctr. for Struct. Biol.
5137 MRB3, 465 21st Avenue S.
Nashville, TN 37232-8755
615-936-2516