From owner-chemistry -A_T- ccl.net Tue Mar 1 10:26:01 2016 From: "Daniel Roe daniel.r.roe ~~ gmail.com" To: CCL Subject: CCL: Overlay structure Message-Id: <-52086-160301102419-17307-V6NwxOS8y3D/m3MROdJqeA+*+server.ccl.net> X-Original-From: Daniel Roe Content-Type: text/plain; charset=UTF-8 Date: Tue, 1 Mar 2016 08:24:13 -0700 MIME-Version: 1.0 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 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)