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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 13 2017 - 11:00:02 PST
