I am trying to compute the rms over a trajectory using the rms command
in ptraj. My rms.in file is below:
ptraj 1500.prmtop << EOF
trajin 1500pcv.nc
reference str.pdb
rms reference mass out spc.rms :1-81.CA time 1.0
EOF
When I run the above script I get the following output:
readAmberRestart (): sscanf on atoms and time in restart file str.pdb
failed
PTRAJ: rms reference mass out spc.rms :1-81.CA time 1.0
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)]
1500pcv.nc: 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 (1500pcv.nc) is a NetCDF AMBER trajectory with box info with 1000
sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
NO ACTIONS WERE SPECIFIED
........25%............................100%
...
What is the statement : "readAmberRestart (): sscanf on atoms and time
in restart file str.pdb failed" telling me?
I have the command "reference" prior to the "rms" command in the script.
Why is it telling me to "set this prior to this rms" and ignoring the
command?
The "readAmberRestart" error message would seem to indicate that the
program is looking for a restart file. I thought that ptraj would use a
pdb file as input to the reference command.
Can someone help me with this?
Thanks!
John
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Received on Wed Jun 16 2010 - 09:00:03 PDT
