AMBER Archive (2008)

Subject: Re: AMBER: GAFF

From: David A. Case (case_at_scripps.edu)
Date: Fri Apr 04 2008 - 10:59:08 CDT

On Fri, Apr 04, 2008, Eric Germaneau wrote:

>
> About torsional part, from amber files format
> <http://amber.scripps.edu/formats.html#parm.dat> one can read that the
> first numerical column is the factor by which the torsional barrier is
> divided.

The gaff torsional information starts at line 4331. The first numerical
column is as described above.

>
> Then the last column is the he periodicity of the torsional barrier, and
> If it is larger than 0.0 then the torsional potential is assumed to
          ^^^^^^^^^^^^ less than!

> have more than one term, and the values of the rest of the terms are
> read from the next cards until a positive is encountered.
>
> * Where are next cards in gaff.dat file?

See lines 4352-4353 for an example of a torsion value with a multiple
periodicity. The "next cards" in this case means line 4353.

>
> * But in the gaff.dat file there are only three columns, not four.

This is true for all force fields. Impropers in gaff start at line 5029.
They have no "first numerical column", because there is no division. It
probably would have been better if 30 years ago, Paul Weiner had just put
a "1" in that column for impropers, (so that "regular" and improper torsions
had the same format) but there you are....

As stated by others, there is no difference between the format of gaff.dat
and the formats of any other Amber parameter files.

...dac
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