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
are
http://www.pymolwiki.org/index.php/Orient
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/
Regards.
Amin.
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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber [1]
Links:
------
[1]
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 01 2015 - 08:30:02 PDT
