Hi,
I often align my molecules along principal axes before solvating. This
can be done quite simply with cpptraj:
parm myparm.parm7
trajin mycoords.rst7
principal * dorotation
trajout rotated.rst7
Hope this helps,
-Dan
On Fri, May 1, 2015 at 8:39 AM, Steven Ramsey <vpsramsey.gmail.com> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri May 01 2015 - 09:30:03 PDT
