VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Jul 12 2006 - 10:56:16 CDT

Dear VMD developers,

Is there a way to change the pdb output from vmd such as to allow
residue numbers greater than 9999 and to eliminate the X chain identifier?

I am trying to save a number of pdb files by selecting "water within 5
of protein" and the pdb output has strange residue numbers such as
X34ef5. The problem with these pdb files is that whenever I try to load
them in other programs, the residues are not recognized anymore. This is
especially painful if I want to use the created pdb files back into the
Leap program from Amber ...

Best wishes
vlad 

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/