On Wed, Feb 16, 2011, vani panguluri wrote:
> http://ambermd.org/tutorials/basic/tutorial4b/
> <http://ambermd.org/tutorials/basic/tutorial4b/>i am following tutorial i
> had apocynin as sustiva and 1k4u as lfko
Sorry: it is not enough to say "I am following the tutorial". You need to try
to provide enough exact information for someone else to reproduce the problem.
The pdb file you attached still has all of the problem hydrogens present. It
is quite different from the 1K4U file from
http://www.rcsb.org.
Your problem arises because you have a very non-standard PDB file that tleap
doesn't know how to deal with, and you don't seem to be able to modify it in
ways that have been suggested here. You should treat this as a learning
experience in how to identify and debug problems that inevitably arise in
carrying out MD simulations. I think you have pretty much reached the limit
of what help can be expected from a mailing list.
....dac
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Received on Wed Feb 16 2011 - 09:30:08 PST
