Hello Anselm,
Thank you! Your suggestion worked perfectly. I used:
unwrap ^1-3
center ^1-3 mass origin
image origin center
and the filament stayed intact now.
Best,
Matthew
> On Jul 15, 2021, at 6:25 AM, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Hi,
>
> if you used iwrap=1 in your simulation, you can simply try to undo this
> by the cpptraj command "unwrap". For this, I'd delete the water
> molecules first and then use the unwrap command without any further
> mask. If this works for you, and you really need not only a continous
> protein system trajectory (for postprocessing) but also a correctly
> imaged system, you may want to temper around with the image command
> afterwards.
> See AmberTools 21 34.11.84 (p. 738)
>
> I had worked with filamentous proteins and often had the issue, that
> single peptide moieties leaving the simulation box where automatically
> wrapped (because I used iwrap=1); when trying the imaging approach, it
> did not work in all my cases (and I essentially tried similar commands
> like you).
>
> Maybe that helps.
>
> Best,
>
> Anselm
>
> NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg
> Germany
>
>
>
>
> On 07/14/2021 05:11 PM, Matthew Guberman-Pfeffer wrote:
>> Hello Dan,
>>
>> Thanks for the reply. I’ve tried autoimage. I’ve also tried specifying the middle domain, or all three domains as the anchor. None of that worked. I’d be glad to share the trajectory if you’d like to take a look.
>>
>> If imaging or autoimaging results in a “broken” structure, how would distance imaging as part of an analysis function not result in the same “broken” structure?
>>
>> Best,
>> Matthew
>>
>>
>>> On Jul 13, 2021, at 1:06 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> *Message sent from a system outside of UConn.*
>>>
>>>
>>> Hi,
>>>
>>> Try 'autoimage' and see if that works for you. You can use it as-is,
>>> or try specifying different expressions for the anchor mask.
>>>
>>> This will only affect calculations that don't automatically perform
>>> distance imaging. The 'hbond' calculation has imaging off by default,
>>> but it can be turned on. Most calculations will automatically image
>>> distances anyway - check the description in the manual to be certain.
>>>
>>> -Dan
>>>
>>> On Tue, Jul 13, 2021 at 10:00 AM Matthew Guberman-Pfeffer
>>> <matthew.guberman-pfeffer.uconn.edu <mailto:matthew.guberman-pfeffer.uconn.edu>> wrote:
>>>>
>>>> Dear Amber Community,
>>>>
>>>> My fairly straight, filamentous protein curled during dynamics, and I’m struggling to find a way to image it back into the box, if possible. I want to post-process the energetics with an implicit solvent, but I’m concerned that the results will be meaningless unless I figure out how to image the protein correctly. Because it’s a homotrimeric complex, I’ve tried the below script for imaging in cpptraj
>>>>
>>>> parm xxx.parm7
>>>> reference xxx.rst7
>>>> trajin xxx.mdcrd
>>>> trajout yyy.mdcrd
>>>>
>>>> center :1-282 mass origin #domain 1
>>>> image origin center
>>>> center :1-564 mass origin #domain 1-2
>>>> image origin center
>>>> center :1-846 mass origin #domain 1-3
>>>> image origin center
>>>>
>>>> But I still get the below (figures attached from 2 different frames). What can/should I try? How much of this issue is a visualization problem and won’t affect a non-periodic (implicit solvent) calculation?
>>>>
>>>> Best regards,
>>>> Matthew
>>>>
>>>>
>>>>
>>>>
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Received on Thu Jul 15 2021 - 07:00:03 PDT
