RE: AMBER: question about amber parameter file format etc.

From: Vineet Pande <>
Date: Wed, 16 Mar 2005 18:06:53 +0000

>What does the first numeric column (after the torsion angle definition)
>represent? Also
is the potention column actually V or V/2?
As an example:
X -CC-CV-X 4 20.60 180.0 2.

first column is the way in which a given torsion can be defined, so, for a
generic case like this you can define in 4 ways and 20.60 is the value of
energy barrier already divided by two. But not divided by 4 (becz it is
shared by 4 torsional definitions in this case, which is indicated in the
first column..if it were an explicit torsion like CA-CA-C-O2, you can write
1 in the first column and the energy barrier than must be divided by 4, and
then by 2 to get what you write in second column....180.0 is the PHASE and 2
is the perodicity (PN)..............More details are found in amber manual,
in the end, on paramterization theory.

About the format of the dat file, most of the other things are obvious angles and bond lengths with the force the end you
have van der Waals parameters ...I am not aware of other documentation of
dat file.

Hope this helps.

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Received on Wed Mar 16 2005 - 18:53:00 PST
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