Hey Dan,
So I figured out that center-image could mask residues; so I tried to
center on residues 153-155 (same results that one molecule is just couldn't
be imaged back...); then I tested with symmetric residues
(153-155,818-820), now each monomer could be imaged successfully; however,
the two dimers are split as one is at the top edge of box and the other is
at the bottom edge of box......According to the original prmtop files, the
complex sits at the center of water box, but also meantime, it sits along
the diagonal line...It seems center-image puts molecule along any of the
side line and that's why it just couldn't fit all back...? But I am so
confused now as why early trajectories could be imaged without any
problem...
Thanks,
Guqin
On Mon, Jul 10, 2017 at 11:43 AM, Guqin Shi <gshi.cop.ufl.edu> wrote:
>
> On Mon, Jul 10, 2017 at 8:32 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
>> 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
>>
>>
> Hi Bill,
>
> Thanks for pointing out the key point of "autoimage". I tried to play with
> autoimage-anchor a little bit by myself. I noticed that the mask for
> autoimage are molecule-wise, instead of residue-wise... Therefore when I
> specify some center residues, cpptraj reports back with error (Error:
> Anchor mask [:153-155] corresponds to 0 mols, should only be 1.) and then
> it goes with default again... Maybe my syntax is somehow not correct?
>
> Also, my system is a little bit special. It is a "dimer" and each monomer
> contains three molecules. There is a hollow in between the two dimers...
> Currently in my own practice, I picked three residues on each of the dimer
> which I think, are the closest to the center of cell (143-155 & 818-820).
> Also, since these residues are symmetric, I am not sure how the program
> would place them in terms of direction...or maybe in this case, asymmetric
> residues might be better...? I attached the prmtop file (with solvens/ions)
> here on my google drive:
> https://drive.google.com/open?id=0B7kncIsWo85ud1BweGJfd1h1ZXM (Since it
> is quite big so I don't think mailing list server would allow that size..)
> Could you also check my system to see if my choice on residues are good or
> maybe another set of residues are better..?
>
>
> Thanks a lot for your help!
> -Guqin
>
> --
> Guqin SHI
> 1345 Center Drive
> College of Pharmacy
> PO Box 100485
> University of Florida
> Gainesville, FL 32610
>
--
Guqin SHI
PhD Candidate in Medicinal Chemistry and Pharmacognosy
College of Pharmacy
The Ohio State University
Columbus, OH, 43210
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Received on Mon Jul 10 2017 - 09:30:03 PDT
