On lines 627 and 629 of
$AMBERHOME/AmberTools/src/mmpbsa_py/MMPBSA_mods/make_trajs.py you can add
"center" to the end of "image origin".
HTH,
Jason
On Sun, Jun 24, 2012 at 9:06 AM, xiaojiong <xiaojiong.zju.edu.cn> wrote:
> 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
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Jun 24 2012 - 08:00:02 PDT
