[gmx-users] RMSD Calculation

[Tsjerk Wassenaar]

Hey :)

You probably want to fit on the protein and calculate the RMSD on the
ligand. You may need to specify these groups in an index file.

Hope it helps,

Tsjerk

On Mar 27, 2011 3:28 AM, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:

Nancy wrote: > > Hi All, > > I need to determine the RMSD of a small
molecule cocrystallized ligan...
I answered this yesterday:

http://lists.gromacs.org/pipermail/gmx-users/2011-March/059697.html

If there's some reason you can't get that to work, then don't simply re-post
the same original question.  Iterative calls to g_rms are quite
straightforward to script.

-Justin

> Thank you very much, > Nancy >
-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
-- 
gmx-users mailing list    gmx-users at gromacs.org
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 gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110327/c747341e/attachment.html>