Re: [AMBER] Solvation of a long protein

From: <>
Date: Fri, 01 May 2015 20:30:08 +0530


Hi. I use the orient functions of pymol or VMD to first align the
protein to the axis and then solvate it. The links to these functions



On 2015-05-01 20:09, Steven Ramsey wrote:

> 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
> dimension?
> Thanks for your time,
> --Steven Ramsey
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Received on Fri May 01 2015 - 08:30:02 PDT
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