[AMBER] Solvation of a long protein

From: Steven Ramsey <vpsramsey.gmail.com>
Date: Fri, 1 May 2015 10:39:38 -0400

Dear Amber Users,

I am attempting to prep a protein in explicit solvent that is a 4 helix
bundle, ~ 100 residues long on each helix. I want to minimize the size of
my solvent box, but it turns out that the pdb of the structure has it
diagonally oriented in space, thus the solvatebox command in leap sets it
in a box where the protein runs along the diagonal.

So I have a two part question: 1) Is there a good way to translate my
protein structure so that it is not diagonal in space (without disrupting
previous work/ introducing strain)?

2) Is there a better shape to use in general for minimizing solvent atom
count, but especially in protein systems that are only large in one

Thanks for your time,

--Steven Ramsey
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Received on Fri May 01 2015 - 08:00:03 PDT
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