AMBER Archive (2008)

Subject: Re: AMBER: GAFF

From: Eric Germaneau (eric.germaneau_at_epfl.ch)
Date: Fri Apr 04 2008 - 12:49:40 CDT

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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> 

-- 
/ Vivre dans la conscience du Tao
Se libérer du mental
<http://www.souffledor.fr/boutique/produits.php?cat=&id=2982>/ --- 
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>
BSP 518
CH-1015 Lausanne
Switzerland
eric.germaneau_at_epfl.ch <mailto:eric.germaneau_at_epfl.ch>
/Tel./: +41 (0)21 / 693 06 36
/Fax./: +41 (0)21 / 693 05 04
/msn/: aihaike_at_hotmail.com
/skype/: aihaike

/ Please consider the environment before printing this email.
Considérez svp l'environnement avant d'imprimer cet email. /

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu