In your second step you need to use a topology that matches the
stripped trajectory. You could repeat the first step, combine all
strip commands into one, and use the 'outprefix' or 'parmout' keywords
to generate a stripped topology. You can also use parmed to generate a
stripped topology (with e.g. strip :WAT,Na+,Cl).
cpptraj input:
parm 1WJB-OPC-FF10-UHm.top
trajin 1WJB-OPC-FF10-UHm.prod40.traj
trajin 1WJB-OPC-FF10-UHm.prod41.traj
strip :WAT,Na+,Cl- outprefix strip
trajout 1WJB-OPC-FF10-UHm-stripWI-40-125.traj
This will give you strip.1WJB-OPC-FF10-UHm.top which you can use with
1WJB-OPC-FF10-UHm-stripWI-40-125.traj.
Also, I recommend using NetCDF trajectories in the future - you can
easily do this by changing 1WJB-OPC-FF10-UHm-stripWI-40-125.traj to
1WJB-OPC-FF10-UHm-stripWI-40-125.nc.
As always, read the manual entries for these commands for full details.
-Dan
On Fri, Oct 21, 2016 at 11:23 AM, Parviz Seifpanahi Shabane
<sparviz.vt.edu> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Oct 21 2016 - 09:30:02 PDT
