Hi,
On Tue, Mar 19, 2013 at 1:28 AM, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
> CPPTRAJ: Trajectory Analysis. V12.1
You're using an out-of-date version of cpptraj, please update your
AmberTools installation (cpptraj should be at least 12.5).
> INPUT: Reading Input from file combined_traj1.in
> [parm /home/gm/Documents/MD/100ns_MD_inputfiles/1PRG_VAC.prmtop [1PRG]]
> [parm /home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_VAC_prosparm.prmtop [FGZ]]
> [trajin /home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1PRG_prostraj.mdcrd.gz]
> [1PRG_prostraj.mdcrd.gz] contains 7500 frames.
> [trajin /home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz [FGZ]]
> Error in box coord line of trajectory
You are not specifying the parm for the last trajin correctly; it's
trying to use the first parm ([1PRG]). The correct way to specify
different topologies with 'trajin' is either 'parm <filename>', 'parm
<tag>', or 'parmindex <#>', so you need:
trajin /home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz
parm [FGZ]
However, this still won't fix your issue since cpptraj currently
checks that an input topology matches the output topology (this
prevents weird problems with non-matching atom/residue names if you're
doing e.g. PDB/Mol2 output). So this line:
> [trajout combined_PPARg_traj.mdcrd.gz nobox]
Will only be valid for trajectories associated with the specified
topology (in this case no topology is specified so it defaults to the
first one loaded, 1PRG).
I can think of one way to get around this, but you should be VERY VERY
CAREFUL. Currently the trajectories and topologies are still different
(# atoms and # residues do not match):
0: [1PRG], 4401 atoms, 270 res, no box, 7500 frames
1: [FGZ], 4468 atoms, 271 res, no box
If you can strip the FGZ topology/coordinates so that the # residues,
# atoms, and atom ordering EXACTLY match 1PRG, you could use the 1PRG
topology to read in the stripped FGZ trajectory as well, then trajout
will work.
Also note that with cpptraj, you can use the 'outprefix <prefix>'
keyword with 'strip' to generate a topology compatible with the
stripped trajectory, e.g.:
parm input.parm7
trajin input.nc
strip :WAT outprefix nowat
trajout nowat.input.nc
will generate nowat.input.parm7, which corresponds with nowat.input.nc.
Good luck,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 20 2013 - 08:30:04 PDT
