[AMBER] cpptraj not processing all mdcrd files

From: Kshatresh Dutta Dubey <kshatresh.gmail.com>
Date: Fri, 25 Jul 2014 00:50:24 +0300

Dear users,

    I am using ambertool 14 to perform lie calculations using cpptraj.
Simulation results have several mdcrd files such as ...run1.mdcrd,
run2.mdcrd........run8.mdcrd. When I am using cpptraj for lie calculations,
it processing only some of the trajectories ( total simulation is about 350
ns but lie output shows for only 11ns) with normal terminations. My cpptraj
input is as :
 trajin ../SF-com-run1.mdcrd
trajin ../SF-com-run2.mdcrd
trajin ../SF-com-run3.mdcrd
trajin ../SF-com-run4.mdcrd
lie :440 :1-439 out lie-SF.dat

as mentioned above, lie-SF.dat shows for 11 ns only while total
trajectories are for 350 ns of simulations. Some initial warning for ptraj
are :
INPUT: Reading Input from STDIN
  [trajin ../SF-com-run1.mdcrd ]
        Reading '../SF-com-run1.mdcrd' as Amber Trajectory
  [trajin ../SF-com-run2.mdcrd]
        Reading '../SF-com-run2.mdcrd' as Amber Trajectory
  [trajin ../SF-com-run3.mdcrd]
        Reading '../SF-com-run3.mdcrd' as Amber Trajectory
  [trajin ../SF-com-run4.mdcrd]
        Reading '../SF-com-run4.mdcrd' as Amber Trajectory
Warning: SF-com-run4.mdcrd: Could not accurately predict # frames. This
Warning: indicates a corrupted trajectory or trajectory/topology
Warning: mismatch. Will attempt to read 1702 frames.
  [lie :440 :1-439 out lie-SF.dat]

Please help me figure out the problem. Same trajectories runs fine for RMSF
and RMSD calculations as well as vmd.
Thanks in advance

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Received on Thu Jul 24 2014 - 15:00:03 PDT
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