Date: Wed, 30 Nov 2016 09:08:00 +0000
Hi Daniel,
Thanks for your suggestion. I used the following script using your guidelines:
Center <protein 1> origin
Image origin center familiar com <protein 1>
Center <protein 2> origin
Image origin center familiar com <protein 2>
Strip :WAT
Strip :NA
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?
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
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(image/png attachment: Distance2.PNG)
