Re: [AMBER] Solvate box

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Fri, 28 Jan 2011 12:53:20 -0800

> How to align it square to the axes, is that in xleap .

Look at it in xleap and see if it's standing on a corner. If so, see
if you can select all and rotate.

Maybe VMD loading prmtop/prmcrd will show the box so you can see if
it hugs the system.

> In packmol I used center of mass to keep my polymer at center of the box.

I doubt that would be a problem, though I haven't used packmol.


AMBER mailing list
Received on Fri Jan 28 2011 - 13:00:03 PST
Custom Search