Basically what I'm doing is pulling a ligand toward a dummy atom. I pull
the ligand until its COM is very close (a few angstroms) from the dummy
atom. Could this be causing this behavior? What information would help?
I'm having a tough time getting the figures attached but may be I could
email them directly to you? Let me know.
Thanks,
- Laura
On 07/02/2012 03:42 PM, Justin A. Lemkul wrote:
On 7/2/12 9:54 AM, Laura Kingsley wrote:
Hello,
I am using steered MD and umbrella sampling to generate a PMF profile for
pulling a small ligand 3 nm. As I pull the ligand from 3A toward 0 A, the PMF
starts a dramatic uphill climb. This does not agree with the force profile
which seems to level out. Any ideas about what might be going wrong here? I am
thinking this probably isn't correct, but I don't know where I've messed up.
Thanks! I can attach the graphs if necessary.
We'll probably need a better description of what you're doing, along with any
applicable figures. It sounds to me like your ligand is crashing into something
in your system, but that's just a guess based on incomplete information.
-Justin
--
Laura Kingsley
Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643
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