Dear Amber User,
I tried to strip the water and Ions from my trajectory, but when I tried to
use the trajectory in another analyze, I got the error (below).
I am using the Amber15.
this my script for strip the water and salt from my trajectory.
-----------------------------------------------------------------------------------------------------
parm 1WJB-OPC-FF10-UHm.top
trajin 1WJB-OPC-FF10-UHm.prod40.traj
trajin 1WJB-OPC-FF10-UHm.prod41.traj
strip :WAT
strip :Na+
strip :Cl-
trajout 1WJB-OPC-FF10-UHm-stripWI-40-125.traj
-------------------------------------------------------------------------------------------------------------
then I tried to use this trajectory "1WJB-OPC-FF10-UHm-stripWI-40-125.traj"
in this script
----------------------------------------------------------------------------------------------------------------
parm 1WJB-OPC-FF10-folded-ref.top
trajin 1WJB-OPC-FF10-UHm-stripWI-40-125.traj
reference 1WJB-OPC-FF10-folded-ref.crd
nativecontacts :1-55&!.H= writecontacts contacts-unfolded.dat out
numcontacts-unfolded.dat reference
------------------------------------------------------------------------------------------------------------------------
and I got this the error message.
-----------------------------------------------------------------------------------------------------------------
"Error: In 1WJB-OPC-FF10-UHm-stripWI-40-125.traj, expect only 3 or 6 box
coords, got 7
Error: Box line=[49.202 70.609 32.533 47.502 72.488 32.981 48.189
]
Error: Could not set up 1WJB-OPC-FF10-UHm-stripWI-40-125.traj for reading.
Error: Could not set up input trajectory '1WJB-OPC-FF10-UHm-stripWI-40-
125.traj'.
1 errors encountered reading input."
Best Regards
Parviz
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Received on Fri Oct 21 2016 - 08:30:03 PDT
