Dear Amber Users,
I know that issue has been posted several times by now, but no matter
nothing works for me.
Sorry for posting this again.
Now the question:
I have a system with a protein bound by a ligand non-covalently.
After running the NVT simulation for 10ns, I was trying to image the system
to wrap the water molecules, but I could not.
The sets of commands I used
I. center :1-54 mass origin
image origin center
II. center :1-54 mass origin
image origin center triclinic
III. center mass origin
image origin center
I was reading earlier posts by various members of the community but still
could not solve the issue. The issue is, not all the water molecules are
wrapped back into the box. Some water molecules still appear outside the
box.
I am using PMEMD of Amber 11 for simulations and ptraj of AmberTools1.5.
Thanks for your time!
Regards
Sai
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Received on Thu Aug 25 2011 - 15:00:03 PDT
