Hi,
Here is the cpptraj input file:
trajin CB-GW-DPP1-ion_equil28.mdcrd 1501 2496 5
center :1-290 mass origin
image origin
strip :HOH:Cl-:DPP
rmsd !(:HOH:Cl-:DPP) mass first
outtraj _MMPBSA_complex.pdb onlyframes 1 nobox pdb
The PDB file shows that the ligand is not in the binding pocket.
Then I change "image origin" to "image origin center" in the input file:
trajin CB-GW-DPP1-ion_equil28.mdcrd 1501 2496 5
center :1-290 mass origin
image origin center
strip :HOH:Cl-:DPP
rmsd !(:HOH:Cl-:DPP) mass first
outtraj _MMPBSA_complex.pdb onlyframes 1 nobox pdb
The new PDB file shows that the ligand is in the binding pocket.
My question is: Why is the ligand not in the binding pocket without "center"?
When I made the free energy decomposition with AmberTool12, the ligand "jump" out of the binding pocket as I examined the _MMPBSA_complex.pdb file. Such problem does not exist in AmberTool1.5.
So I think the problem might exist in the cpptraj command! What can I do if I want to add "center" into cpptraj input file? Would you please be kind enough to give me some advice? Looking forward to your reply. Many thanks!
Sincerely yours, Xiao Jiong
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jun 24 2012 - 06:30:03 PDT
