OK, after reviewing the files you gave me I think that autoimage is
working correctly - your ligand has just drifted far from the
receptor. If you use the 'distance' command (which calculates
distances according to the minimum image convention by default) you
will see the distances for the frames you gave me between e.g. residue
388 (which appears near where you want the ligand to be on the
receptor) and the receptor (residues 395-399) are 62.5505, 64.6322,
65.4063, and 65.5229.
-Dan
On Tue, Jan 17, 2017 at 9:38 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I received your files and just though of one more thing to try. What
> happens if you add the 'origin' keyword to the autoimage command
> (using a suitable anchor like :388 or something)?
>
> -Dan
>
> On Fri, Jan 13, 2017 at 1:50 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> Hi,
>>
>> In order to help further I will need to try and run the imaging
>> myself. Can you send me off-list your topology and a few of your
>> problematic frames? For example, if you know that frames 7, 10, and 23
>> are not properly imaged you could do:
>>
>> parm myparm.parm7
>> trajin mytraj.nc
>> trajout problem.nc onlyframes 7,10,23
>>
>> Also, if you could provide me with a frame that looks the way you
>> expect that would be helpful. Thanks,
>>
>> -Dan
>>
>> On Fri, Jan 13, 2017 at 12:09 AM, colvin <colvin4367.gmail.com> wrote:
>>> Dear Dan,
>>>
>>> I have downloaded and compiled ccptraj from github, now i can anchor only a
>>> certain part of my receptor. However, in one of my system, this doesn't
>>> solve the imaging problem. I have tried selecting different parts of my
>>> receptor. I read in one of your response in the archive, you mentioned
>>> about this:
>>>
>>> center <interface 1 mask> origin
>>> image origin center familiar com <interface 1 mask>
>>> center <interface 2 mask> origin
>>> image origin center familiar com <interface 2 mask> <mask excluding protein
>>> 1>
>>>
>>> this is exactly what i want, to image the receptor first then the peptide
>>> but still it cannot solve the problem. Is there a way that autoimage can
>>> simultaneously image two molecules? I mean the whole complex.
>>>
>>> Thanks!
>>>
>>> On Mon, Jan 9, 2017 at 10:40 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>>> On Mon, Jan 9, 2017 at 3:10 AM, colvin <colvin4367.gmail.com> wrote:
>>>> > My system consisting a receptor/protein and a peptide. The trajectories
>>>> > post-
>>>> > autoimage produced multiple jumps in the rmsd plot for the whole system
>>>> > (receptor+peptide) - plot1. I can see that my peptide is jumping around
>>>> the
>>>> > protein (corresponds to the jump in the plot) when I viewed the
>>>> > post-autoimage trajectory in VMD.
>>>> >
>>>> > However, if only the peptide or receptor rmsd is plotted, there is no
>>>> such
>>>> > jump as observed in the plot1. Without autoimage, the peptide wanders far
>>>> > from the receptor at certain timestep, when viewing it with the VMD
>>>>
>>>> This makes sense if autoimage is not working well for your system. If
>>>> you are calculating the RMSD of a single molecule, imaging by molecule
>>>> has no effect. There is only an issue when you calculate the RMSD of
>>>> multiple molecules since they may be imaged differently (which causes
>>>> jumps).
>>>>
>>>> An improvement was recently made to the 'autoimage' command in the
>>>> GitHub version of cpptraj: https://github.com/Amber-MD/cpptraj
>>>>
>>>> You can use the 'anchor' mask to specify only a small number of atoms
>>>> that should remain near the center of your unit cell - this improves
>>>> the performance of 'autoimage' in tightly packed systems.
>>>>
>>>> -Dan
>>>>
>>>> >
>>>> > Pls advise. Thanks.
>>>> >
>>>> > *Plot1:*
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > *rmsd_receptor:*
>>>> >
>>>> >
>>>> >
>>>> > *rmsd_peptide:*
>>>> >
>>>> > _______________________________________________
>>>> > AMBER mailing list
>>>> > AMBER.ambermd.org
>>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>>> -------------------------
>>>> Daniel R. Roe
>>>> Laboratory of Computational Biology
>>>> National Institutes of Health, NHLBI
>>>> 5635 Fishers Ln, Rm T900
>>>> Rockville MD, 20852
>>>> https://www.lobos.nih.gov/lcb
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Jan 17 2017 - 08:00:02 PST
