Thank you for your help!
It's clear.
David A. Case wrote:
> 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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>
--
/ Vivre dans la conscience du Tao
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Thierry Chaïbli ---
Dr. Éric Germaneau <http://dantian.free.fr>
Ecole polytechnique fédérale de Lausanne (EPFL)
FSB - IPMC
Laboratoire de Cristallographie (LCr) <http://lcr.epfl.ch>
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Received on Fri Apr 18 2008 - 21:16:49 PDT
