AMBER Archive (2006)

Subject: Re: AMBER: set a trucated octahedron box in Leap

From: Vlad Cojocaru (
Date: Tue Sep 12 2006 - 03:30:06 CDT

Thanks David for the answer,

Of course I did that but the problem is that I need also a top file
which contains the periodicity info ... Without box info in the top
file, periodic MD wont run ... So, I will set the IFBOX to 2 and then
copy the %FLAG BOX DIM from the initial top file ... Is there anything
else I should consider?

Best wishes

David A. Case wrote:

>On Mon, Sep 11, 2006, Vlad Cojocaru wrote:
>>I have an equilibrated periodic system (truncated octahedron box) and I
>>want to do a very small modification of the system using Leap. In the
>>meantime I want to retain all info regarding periodicity (box shape and
>For truncated octahedron, you probably will have to manually edit the last
>line of the coordinate file to match what was there in the earlier file
>(before the change).
>...good luck...dac
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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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