On 10/20/13 9:13 AM, sunyeping wrote:
Dear gromacs users, I am studying gromacs umbralla sampling. I want to pull a
lingand out of its binding pocket in a protein. By observing the
ligand-protein complex, I think I should pull the ligand along a direction
which is not parallel to the x, y or z axis so as to prevent the ligand
colliding with the atoms around the the pocket. So I have to define a box
whose long axis is parallel to the pulling direction. Could anyone explain to
me that how to define the box?Thanks in advance!
You don't define the box around the solute, per se, but you orient the solute
within the box. Simple rotation with editconf -rotate should align your active
site channel with a Cartesian axis.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
==================================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
