Hi,
Just following up on this so it makes it to the mail archive.
I've come up with an improvement to 'autoimage' that made it work for
Mark's system, and hopefully tightly packed systems in general. What
I've done is modify the 'anchor' mask keyword so one can specify a
smaller region of the anchor molecule to center on; this should in
effect preserve interface regions. I tried Mark's system with
'autoimage origin anchor :96' (I chose TRP96 because it's close to the
interface that should be preserved) and all problem frames were
successfully imaged.
The updated code is available via GitHub: https://github.com/Amber-MD/cpptraj.
Comments are welcome.
-Dan
On Thu, Dec 1, 2016 at 6:37 AM, Mark Waterhouse [RPG] <ummwa.leeds.ac.uk> wrote:
> Hi Daniel,
>
> I've tried imaging with your suggestion but for some reason I can't get the "not" mask to work (I'm a bit of a novice with AMBER). This is why my script is producing:
>
> Reading 'G3_3A_wat.top' as Amber Topology
>> trajin G3_3A_wat.md14.x
> Reading 'G3_3A_wat.md14.x' as Amber Trajectory
>> center :1-172 origin
> CENTER: Centering coordinates using geometric center of atoms in mask (:1-172) to
> coordinate origin.
>> image origin center familiar com :1-172
> IMAGE: By molecule to origin based on center of mass using atoms in mask *
> Triclinic On, familiar shape centering on atoms in mask :1-172.
>> center :173-260 origin
> CENTER: Centering coordinates using geometric center of atoms in mask (:173-260) to
> coordinate origin.
>> image origin center familiar com :173-260 !:1-172
> IMAGE: By molecule to origin based on center of mass using atoms in mask !:1-172
> Triclinic On, familiar shape centering on atoms in mask :173-260.
>
> Am I doing this command right or not? I just can't seem to tell cpptraj to not include the first protein!
>
> Thanks for all of your help,
>
> Mark
>
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: 30 November 2016 18:25
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Fw: Problems with imaging
>
> On Wed, Nov 30, 2016 at 4:08 AM, Mark Waterhouse [RPG] <ummwa.leeds.ac.uk> wrote:
>>
>> I've attached a picture of the same distance as before - I'm still seeing the same problem. I wasn't sure if I'd included your suggestion of <mask excluding protein 1> as I wasn't entirely sure what that meant. So maybe I have accidentally moved the first protein out of the box. What would be the mask to exclude protein 1 if I haven't included it already?
>
> Just use the 'not' symbol, '!', to negate a mask. So if ':1-56' is protein 1 then specify '!:1-56' to exclude protein 1.
>
> -Dan
>
>>
>>
>> Thanks,
>>
>> Mark
>>
>> -----Original Message-----
>> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
>> Sent: 29 November 2016 14:00
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] Fw: Problems with imaging
>>
>> Hi,
>>
>> Hm, seems like a challenging system. One thing you could try is to manually image each protein using 'image' and the 'com' keyword so that interface atoms are more or less centered in the unit cell. Maybe something like:
>>
>> 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>
>>
>> The <mask excluding protein 1> is to make sure the second 'image'
>> command doesn't try to move the first protein out of the box again.
>> Also, could you send me off-list a topology and some of the trajectory frames which don't get imaged properly (i.e. frames corresponding to the high distances in your plot)? I'll try to improve the 'autoimage'
>> command to handle cases like yours. Thanks,
>>
>> -Dan
>>
>>
>> On Mon, Nov 28, 2016 at 3:49 PM, Mark Waterhouse [RPG] <ummwa.leeds.ac.uk> wrote:
>>> Dear AMBER users,
>>>
>>>
>>>
>>> I'm hoping you can help me with imaging my system. My system consists of two interacting proteins - including repeats and variations of my proteins I have about 18 trajectory files. Normally, the two proteins end up separating from each other, with one of the interacting partners moving into a different box. I have had a large amount of success using autoimage in cpptraj to image 16/18 of them, but the remaining two are giving me a lot of problems. The problem seems to be the "ligand" protein jumping out of the periodic box. I've attached an example of what's happening using a bond distance between the interface of the two proteins. It might also be useful to note that my system won't RMS fit because the proteins move around the box.
>>>
>>>
>>>
>>> [cid:image001.png.01D244A8.66C24D50]
>>>
>>>
>>>
>>> My usual script would look something like this:
>>>
>>>
>>>
>>> Parm x.top
>>>
>>> Trajin simulation.x
>>>
>>> Autoimage
>>>
>>> Strip :WAT
>>>
>>> Strip :NA
>>>
>>> Trajout file.x
>>>
>>>
>>>
>>> I've tried several variations on this to try and solve the problem, e.g.
>>>
>>>
>>>
>>> Autoimage :1-172 or :173-260 (which are each protein respectively). I've also included the anchor command before specifying the mask as well with no luck.
>>>
>>>
>>>
>>> I've also tried the following commands in different orders to see if that would solve the problem - still with no luck.
>>>
>>>
>>> Autoimage
>>>
>>> Center :1-260 mass origin (or :1-172/:173-260 as above)
>>>
>>> Image origin center familiar
>>>
>>>
>>>
>>> I've exhausted all of the previous solutions to problems on the reflector and don't know what to try next. Any ideas?
>>>
>>>
>>>
>>> Many thanks,
>>>
>>>
>>>
>>> Mark Waterhouse [RPG]
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>
> _______________________________________________
> 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 Jan 09 2017 - 06:30:04 PST
