Hi,
You're seeing the solvent and ions left over because you never applied a
strip mask- the line you'd actually want to run is
strip WAT:Na+
To remove the extra stuff, and put it after you load your trajectory and
before you write the output.
Best,
Kenneth
On Thursday, December 17, 2015, shahab shariati <shahab.shariati.gmail.com>
wrote:
> Dear amber users
>
> My system contains protein (residues 1-314) + ligand (residue 315) + Na
> ions (residues 316-323) + water molecules.
>
> After doing MD simulation using amber tools 14, I have 4000 frames.
>
> Now, I need to a trajectory containing only protein + ligand molecules
> (residues 1-315) and only frames 3950 and 4000.
>
> I have runned cpptraj in batch mode using following in files:
>
> parm comp_sol.prmtop
> trajin trajectory.binpos 3950 4000
> trajout 6.pdb pdb :1-315
>
> parm comp_sol.prmtop
> trajin trajectory.binpos 3950 4000 :1-315
> trajout 6.pdb pdb
>
> But both cases give me a trajectory in which there are protein + ligand +
> Na + water molecules instead of only protein + ligand molecules.
>
> How to do what I want.
>
> Any help will highly appreciated
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Received on Thu Dec 17 2015 - 07:00:03 PST
