Dear all,
I was reading this message in the mailing list:
http://archive.ambermd.org/200809/0147.html and this tutorial:
http://ambermd.org/doc6/html/AMBER-sh-4.3.html about the refinement in
explicite water solvent.
For the moment, I have a protocol which works well in vacuum to
determine NMR structures and now I would to add a refinement in water
solvent step, starting from my set of structures. For each structure, I
have to run leap to design the solvent box.
e.g. in leap:
gcg=loadpdb gcg.pdb (read in starting structures)
addions gcg Na+ (neutralize system with sodium counterions)
solvatebox gcg WATBOX 216 9.0 0.8 (put in explicit water)
saveamberparm gcg prmtop gcg_start.x (save topology and AMBER coordinate
files)
How can I ask leap to automatically take each structure and create
parameter and coordinate files? What is the best way to link the steps
in vacuum and the final refinement in water? Thanks.
Best regards,
Baptiste
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Received on Wed Sep 29 2010 - 06:30:03 PDT
