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
>>>
>> _______________________________________________
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>
>
>
> --
> -------------------------
> 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 - 07:00:04 PST
