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 - 06:30:03 PST
