Dear Amber community,
I aim to work on MD simulation of methylated DNA with AMBER 9. Would you
please give me some information regarding the addition of methyl
groups to my .pdb file. I don't know how can I
add methyl groups to my .pdb file. Output file (.pdb) of
http://w3dna.rutgers.edu/ [
http://w3dna.rutgers.edu/],
nucgen or nab hasn't any hydrogen atom to exchange it with carbon. I don't
think but can I exchange hydrogen
atoms with carbon in the output pdb file of LEaP and then again let
LEaP to add the extra hydrogens?
Regards,
Ehsan
--------------------------------------------------------------
Ehsan Habibi
M.Sc. candidate of Biophysics
Laboratory of Systems Biology and Bioinformatics (LBB)
Institute of Biochemistry and Biophysics (IBB)
University of Tehran,Tehran, Iran.
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Received on Tue Jun 15 2010 - 10:30:22 PDT
