Hi,
The key for 'autoimage' is that you need to specify a region
(molecule, residue, atom, etc) that visually you want to be at the
center of your unit cell; in cpptraj this is called the 'anchor'. By
default 'autoimage' tries to use the first molecule to do this.
However in certain systems another choice is better. For example, if
you have a dimer then you would want to choose 1 or more residues that
are near the center of the interface between the two monomers as your
anchor. Without seeing your system I can't make specific
recommendations, but you could try experimenting with different anchor
points. If you'd like, send me a PDB file or topology/restart files of
your system off-list and I can try to recommend an anchor.
-Dan
On Sat, Jul 8, 2017 at 10:06 PM, Guqin Shi <shi.293.osu.edu> wrote:
> Hi Dan,
>
> Thanks for reply.
> Yes, the first I've thought of is to use "autoimage" directly. I have to
> admit it worked unexpectedly well. But for the late ns trajectories, it
> failed, too. It has the same result as the one I got from the separate
> center-and-image...
>
> Best,
> Guqin
>
> On Sat, Jul 8, 2017 at 8:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> Try the 'autoimage' command in cpptraj and see if that works for you.
>>
>> -Dan
>>
>> On Sat, Jul 8, 2017 at 6:59 PM Guqin Shi <shi.293.osu.edu> wrote:
>>
>> > Dear all,
>> >
>> > My simulation is on a huge complex containing 6 molecules. To visualize
>> the
>> > trajectory and get "correct" coordinates, I usually center-n-image the
>> > coordinates... I used to center on 1 molecule, image, and then center on
>> 2
>> > molecules (include the first one), and then image; and eventually center
>> on
>> > 6 molecules and image, as suggested in some amber mailing list posts. It
>> > worked well.
>> >
>> > ex.
>> > center :1-300 origin (molecule 1)
>> > image center origin
>> > center :1-500 origin (molecule 2)
>> > image center origin
>> > center :1-650 origin (molecule 3)
>> > image center origin
>> > center :1-950 origin (molecule 3)
>> > image center origin
>> > center :1-1150 origin (molecule 4)
>> > image center origin
>> > center :1-1300 origin (molecule 6)
>> > image center origin
>> >
>> > However, as the molecules deviates during the simulation, after applying
>> > the above commands, there is always one molecule (it could be different
>> > molecule dependent on the order I center-image on different masks...)
>> that
>> > just couldn't be placed back... no matter how different combinations I
>> have
>> > tried...
>> >
>> > My first question is that does it make sense that the above commands work
>> > well for first quite a few ns of trajectories but failed to wrap for the
>> > late ns of trajectories...?
>> >
>> > The second one will be if there is any tips or suggestions or starting
>> > point that I could try out? I have tried different combinations, starting
>> > center on different molecule(s), I just couldn't get all 6 back to the
>> > correct place...
>> >
>> > I also tried to center on reference structure...but it just put molecule
>> > onto the geometric center, the direction is still off...I don't know how
>> to
>> > center molecules onto a suitable place so that all 6 could be fit into
>> one
>> > box...That doesn't make sense...I mean I start with an intact complex...
>> >
>> >
>> > Thank you for any thoughts!
>> > Best,
>> > Guqin
>> >
>> >
>> >
>> > --
>> > Guqin SHI
>> > PhD Candidate in Medicinal Chemistry and Pharmacognosy
>> > College of Pharmacy
>> > The Ohio State University
>> > Columbus, OH, 43210
>> > _______________________________________________
>> > 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
>>
>
>
>
> --
> Guqin SHI
> PhD Candidate in Medicinal Chemistry and Pharmacognosy
> College of Pharmacy
> The Ohio State University
> Columbus, OH, 43210
> _______________________________________________
> 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
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Received on Mon Jul 10 2017 - 06:00:05 PDT
