[Chimera-users] WriteDMS with cofactors?

Walter Novak wnovak at brandeis.edu
Mon Mar 9 18:25:37 PDT 2009

Hi All,

I seem to have trouble with the dock prep procedure for molecules with  
cofactors, specifically NADP+. I cannot figure out how to write out  
the surface of both the protein and cofactor together. I can do this  
with the standalone DMS program using the "-a" flag. Am I missing  
something? I am using pdb 1el3 as a test and trying to redock the  
inhibitor I84 back into the complex. I completed the tutorial using  
1abe and this was very valuable in learning how to prep molecules with  


Walter R.P. Novak, Ph.D.
Postdoctoral Fellow
Rosenstiel Basic Medical Research Center
Brandeis University
415 South St. MS 029
Waltham, MA 02454-9110
Phone: (781) 736-4944
Fax: (781) 736-2405

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