Hi everybody
I've been using the script <measure_equil_rmsd.ptraj> (Tutorial3:http://ambermd.org/tutorials/advanced/tutorial3/section1.htm)
trajin equil_2ns.mdcrd.gz 1 1000 1
reference myfile_solv.inpcrd
rms reference out equil.rmsd .CA,C,N
The script processes the input files but produces NO equil.rmsd output.
The weird thing is that the same script has worked previously with success.
Comparing terminal output (see below) with earlier successful ones, the difference is in WARNING but I can't figure out why.
Thanks for any help in advance
George
PTRAJ: Processing input from file measure_equil_rmsd.ptraj
PTRAJ: trajin equil_2ns.mdcrd.gz 1 1000 1
Checking coordinates: equil_2ns.mdcrd.gz
Rank: 0 Atoms: 27381 FrameSize: 665384 TitleSize: 81 NumBox: 3 Seekable 1
PTRAJ: reference 2ogn_3og_solv.inpcrd
PTRAJ: rms reference out equil.rmsd .CA,C,N
WARNING in ptraj(), rms to reference: missing reference structure.
Set this prior to this rms with the command "reference"
Ignoring command...
[No output trajectory specified (trajout)]
equil_2ns.mdcrd.gz: 1000 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 1000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (equil_2ns.mdcrd.gz) is an AMBER trajectory (with box info) with 1000 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
NO ACTIONS WERE SPECIFIED
Processing AMBER trajectory file equil_2ns.mdcrd.gz
1% ............ 25% ............ 50% ............ 75% ............ 100%
PTRAJ: Successfully read in 1000 sets and processed 1000 sets.
Dumping accumulated results (if any)
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Received on Wed Jan 05 2011 - 08:30:03 PST
