dear amber specialists,
since Im obout to do a 100 ns simulation (pmemd, Amber8), I have to cut my tajectory for analysis. I tried this via ptraj:
ptraj sh3_cryst_water_ions.top sh3_cryst_long_cut.ptraj
with sh3_cryst_long_cut.ptraj:
trajin ./sh3_cryst_NTV_100200ps_orest.mdcrd
trajout ./sh3_cryst_long_1_1000.mdcrd
go
The output was the following:
[...]
Successfully completed readParm.
PTRAJ: Processing input file...
Input is from file sh3_cryst_long_cut.ptraj
PTRAJ: trajin ./sh3_cryst_NTV_100200ps_orest.mdcrd
Checking coordinates: ./sh3_cryst_NTV_100200ps_orest.mdcrd
Could not open file (./sh3_cryst_NTV_100200ps_orest.mdcrd) with mode (r)
WARNING in checkCoordinates(): Could not open file (./sh3_cryst_NTV_100200ps_orest.mdcrd)
WARNING in ptrajSetupIO(): trajin ./sh3_cryst_NTV_100200ps_orest.mdcrd, cannot open file...
PTRAJ: trajout ./sh3_cryst_long_1_1000.mdcrd
WARNING in ptraj(): No input trajectories specified (trajin), aborting...
I tested AMBER7 as well as AMBER8 ptraj and checked several times whether the input file exists. What might be the reason? Are there problems with detecting a pmemd trajectory file, or is something wrong with the extension to hinder autodetection?
regards,
Anna
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Received on Sun Aug 06 2006 - 06:07:10 PDT
