Thanks!
Those were useful tips/tricks + scripts, I really appreciate it,
--Steven Ramsey
On Fri, May 1, 2015 at 12:09 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri May 01 2015 - 10:00:04 PDT
