What's needed is an image minimizer that tries all neighboring box
placements for all molecules.
Bill
On 7/8/17 7:06 PM, Guqin Shi 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
>>
>
>
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Received on Sat Jul 08 2017 - 19:30:03 PDT
