CCL: Overlay structure
- From: Daniel Roe <daniel.r.roe:gmail.com>
- Subject: CCL: Overlay structure
- Date: Tue, 1 Mar 2016 08:24:13 -0700
Sent to CCL by: Daniel Roe [daniel.r.roe|gmail.com]
Hi,
If you would like a scriptable way to do this you could use CPPTRAJ,
part of the freely available AmberTools
(http://ambermd.org/AmberTools15-get.html).
For example, if your X-ray structure is called X-ray.pdb and your
optimized structure is called Opt.pdb, you could use the following
commands in CPPTRAJ to perform a best-fit alignment and calculate RMSD
for all CA atoms:
parm X-ray.pdb
reference X-ray.pdb
trajin Opt.pdb
rms ToRef reference ]_[CA out rmsd.dat
trajout Aligned.pdb
go
The structure of Opt.pdb aligned on X-ray.pdb will be written to
Aligned.pdb, and the RMSD will be written to 'rmsd.dat'. You can also
calculate the per-residue RMSD if desired via the 'perres' keyword.
Hope this helps,
-Dan
On Mon, Feb 29, 2016 at 12:34 PM, Saied Mohammed Soliman
saied1soliman%yahoo.com <owner-chemistry]_[ccl.net> wrote:
>
> Sent to CCL by: "Saied Mohammed Soliman"
[saied1soliman__yahoo.com]
> Hello colleagues,
> I need a free and user friendly software to overlay the optimized structure
> with the X-ray structure in order to compare the matching between them,
> anyone could help me.
> Thanks
> Saied>
>
--
-------------------------
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)