AMBER Archive (2008)

Subject: Re: AMBER: imaging problem

From: Marcin Krol (krol01_at_cancer.org.uk)
Date: Tue Apr 15 2008 - 08:38:07 CDT

Yes, you're right, I checked if box info is present in the traj file,
but forgot that I'm using a parm file without box info!!!
Thanks a lot
Marcin
> Marcin,
>
> I had a similar problem once.
>
> Make sure your stripped topology contains a box as well. It seems that
> this sets some flag in ptraj without which the imaging doesn't work
> properly.
>
> I can't remember anymore whether I used modifyBoxInfo in rdparm or
> manually added the box in leap. Both should do the trick.
>
> Good luck.
>
> David.
>
>
>
> On Tue, 2008-04-15 at 14:16 +0100, Marcin Krol wrote:
>
>> Thanks
>> It works beautifully on original trajectories (protein+water+ions,
>> trajectory file with PBC info). However, it doesn't work on trajectories
>> with removed water and ions but _with_ PBC info present (I generated no
>> water trajectories without nobox keyword). Don't know why, but at least
>> it works for the original ones
>> Many thanks
>> Marcin

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu