AMBER Archive (2000)

Subject: Re: HEllo!

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Sat Sep 30 2000 - 11:36:51 CDT

> I was just wondering if anyobe can tell me how to FIT the RMSD of the
> coordinate set (i+1) to the coordinate set (i) in CARNAL? In the other
> word, I have a trajectory contained many snapshots and I want to compute
> the RMSD of the snapshot (i+1) against the snapshot (i) rather than
> compute the RMSD of snapshot (i+1) against the first snapshot or the one
> defined as STATIC. Thanks for your help!

ptraj, also supplied with AMBER (or available in current form from
   http://hnu.pharm.utah.edu/medchem/cheatham/ptraj.tar.Z),
can do this with the rms "previous" option. For a given set of
trajectories (mdcrd.1, mdcrd.2.Z, mdcrd.3), to create a trajectory
called "mdcrd.fitprevious", outputing the RMSd vs. time to a file
called "rms.dat" with a time interval between frames (for the output
file) of 0.5 ps, fitting residues 1-20 atom names C, CA and N, the script
would look like:

trajin mdcrd.1
trajin mdcrd.2.Z
trajin mdcrd.3
trajout mdcrd.fitprevious
rms previous mass out rms.dat interval 0.5 :1-20_at_C,CA,N
go

You could run this by putting this commands into a file ptraj_rms.in and
run

ptraj prmtop ptraj_rms.in

For more information, read the ptraj.html documentation file
  (http://hnu.pharm.utah.edu/medchem/cheatham/ptraj.html)

Thomas E. Cheatham, III
Assistant Research Professor
Department of Medicinal Chemistry & Center for High Performance Computing
University of Utah INSCC 418
30 South 2000 East, Room 201 155 South 1452 East
Salt Lake City, Utah 84112-5820 Salt Lake City, Utah 84112-0190
tom.cheatham_at_pharm.utah.edu cheatham_at_chpc.utah.edu
FAX: (801) 585-9119 FAX: (801) 585-5366
phone: (801) 587-9652