[AMBER] MD simulation of methylated DNA: addition of methyl groups to .pdb file

From: Ehsan Habibi <EHabibi.ibb.ut.ac.ir>
Date: Tue, 15 Jun 2010 21:53:45 +0430

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?


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
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