[AMBER-Developers] Auto-image code in Cpptraj

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 6 Jun 2012 18:16:32 -0400

Hi All,

I've implemented a new command in GIT/master cpptraj named
'autoimage'. The intent is to take most of the frustration out of
imaging and have it just "work". An example of the usage is:

parm test.parm7
trajin test.nc
trajout test.nc

Note also that 'trajout' will now automatically determine output traj
format via filename extension if no keyword is given (in this example
netcdf traj). Recognized extensions are .nc, .ncrst, .pdb, .mol2,
.dcd, .rst7, .crd.

I have tested the code on a trajectory with split-up DNA molecules and
it put them back together nicely. If anyone has any problematic
trajectories (especially things like tetramers etc) and would like to
give it a try I'd be interested to hear if it worked for you or not.
Alternatively, if anyone would like to provide me with the
topology/trajectory to test myself that would be appreciated as well.


Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
AMBER-Developers mailing list
Received on Wed Jun 06 2012 - 15:30:02 PDT
Custom Search