Dear Colvin,
the RMSD plots for no-center-no-image and autoimage look the same to me.
Although the graph exhibits a large increase in the area of interest
(your red arrow), it looks different from graphs I've seen before
typical for the imaging issue. However, the RMSD at that time is nearly
10 A, so you probably may not see any large differences in the absolute
value.
My suggestions are:
- Watch the trajectory movie carefully, i.e. step by step in the
respective region, in order to spot a potential instantaneous jump of
the ligand.
- Plot the distance between two CA atoms from the ligand and protein
over time; an imaging problem could also be identified in a jump of the
curve.
- Compute the RMSD with respect to each previous frame vs time. Again,
an imaging issue should result in a larger jump.
- Try the command unwrap on the original trajectory (but after stripping
off the solvent) in order to cancel the effects introduced by automatic
wrapping and then perform the RMSD fit and calculation.
Maybe that helps.
Regards,
Anselm
Am 17.06.2016 09:06, schrieb colvin:
> Sorry, the images do not attached correctly, I'm inserting them again.
> Thank you
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> On Fri, Jun 17, 2016 at 3:02 PM, colvin <colvin4367.gmail.com> wrote:
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>>
>> Hello all,
>>
>> Thank you for your reply, I have read the papers as suggested, and i found
>> that the peak in my rmsd plot is somewhat different than the one shown in
>> the paper. So i am suspecting that my peptide did dissociate from the
>> receptor... and this is strange, as the peptide was shown to has highest
>> inhibition activity compare to others.
>>
>> I did some experiment using 1. autoimage, 2. center origin + image
>> familiar, and 3. without any reimage keyword.
>>
>> The rmsd plots for the autoimage and without reimage keyword are
>> identical, but the one using center origin + image familiar has no sharp
>> peak towards the end of the graph (red arrow). I am not sure why... The
>> rmsd plots for peptide alone and receptor alone are all identical for the
>> three cases.
>>
>> The trajectory movie without any processing, showed that the peptide
>> dissociated, and the trajectory with autoimage processing, also showed that
>> the peptide dissociated, but the peptide was at the other side of receptor
>> (see image, location 3). I feel strange, and confuse...
>>
>> Pls enlighten me. Thank you!
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>> On Thu, Jun 16, 2016 at 6:31 PM, Dr. Anselm Horn <anselm.horn.fau.de>
>> wrote:
>>
>>>> I am simulating a peptide that has known activity to a receptor, but
>>>> throughout the 20ns simulations, the peptide is no longer at the binding
>>>> site, pls see the image below, on how the peptide moved out from the
>>>> binding site to location 3.
>>>>
>>>> Is this something to do with the trajectory imaging? I have tried 1.
>>>> autoimage and 2. center, image familiar, and both gave the same output.
>>>>
>>>> Or the peptide just doesn't fit to the binding site? The energy at the
>>> last
>>>> .out file is still negative.
>>>
>>> Normally, you can distinguish a true dissociation event from an imaging
>>> issue by watching the trajectory in a viewing program (like VMD):
>>> dissociation occurs most often in several visible steps (unless your
>>> frame intervall is too large and your bound ligand too small), whereas
>>> imaging causes an instantaneous, several Angstroem-long jump of the
>>> ligand between two trajectory frames, i.e. from one side of the
>>> simulation box to the other.
>>>
>>> Another hint is the graph RMSD vs time: If you observe instantanous
>>> jumps in the plot of serveral Angstroems in height, this is indicative
>>> of an imaging issue. (See e.g. DOI 10.1007/s00044-014-1135-5 for an
>>> illustration of the imaging topic.)
>>>
>>> The energy in the out file is the total system energy including the
>>> solvent-solvent and solvent-solute contribution; thus it cannot used
>>> simply to monitor dissociation events. For this, you could utilize the
>>> linear interaction energy (LIE) between the ligand and the parent
>>> protein, easily calculated via cpptraj: In case of a dissociation, a
>>> gradual decrease of interaction energy is expected.
>>>
>>> Regards,
>>>
>>> Anselm
>>>
>>>
>>>
>>>
>>>
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>>>
>>
>>
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Received on Fri Jun 17 2016 - 04:00:02 PDT
