Re: AMBER: imaging problem

From: Marcin Krol <>
Date: Tue, 15 Apr 2008 14:38:07 +0100

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,
> 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

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Received on Fri Apr 18 2008 - 21:19:32 PDT
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