AMBER Archive (2008)

Subject: Re: AMBER: GAFF

From: Eric Germaneau (eric.germaneau_at_epfl.ch)
Date: Fri Apr 04 2008 - 03:27:07 CDT

You're right, my question was the following:

Dear Amber users,

I've begun to use GAFF and there are some feature of the /gaff.dat/ file
that I do not understand.
Information about file formats, and what various columns mean, is given
in the "file formats" link at the Amber web page but it doesn't fit the
GAFF function form
<http://amber.scripps.edu/antechamber/gaff.html#function>.

One can read the following in the torsional part:

*...
X -c -c -X 4 1.200 180.000 2.000
X -c -c1-X 2 0.000 180.000 2.000
X -c -cg-X 2 0.000 180.000 2.000 same as
X-c-c1-X
X -c -ch-X 2 0.000 180.000 2.000
...
*
>From amber files format <http://amber.scripps.edu/formats.html> one
can read that the first numerical column is the factor by which the
torsional barrier is divided. What is the link with the GAFF function
form <http://amber.scripps.edu/antechamber/gaff.html#function>? 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 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?

Then, the negative value is used only for identifying the existence of
the next term and only the absolute value is kept.

Can someone can explain to me what does it mean and if it makes sense in
GAFF?

About improper parameters one can read:*

...
X -o -c -o 1.1 180. 2. JCC,7,(1986),230
X -X -c -o 10.5 180. 2. JCC,7,(1986),230
X -X -cz-X 10.5 180. 2. Just for
guadinium, Junmei 2006
X -X -ca-ha 1.1 180. 2. bsd.on C6H6
nmodes
...
*
What is the expression of the improper potential in GAFF?

>From amber files format <http://amber.scripps.edu/formats.html> one
can read that the input is the same as in for the dihedrals except that
the torsional barrier height is NOT divided by the first numerical
column. But in the gaff.dat file there are only three columns, not four.

Below improper parameters, one can see the van der Waals parameters I
guess, A_i and B_i.

Do we have A_ij = square_root( A_i * A_j ) ?

Vlad Cojocaru wrote:
> Hi Eric,
>
> Maybe it would help if you also repost your question ...
>
> vlad
>
> Eric Germaneau wrote:
>> Dear all,
>>
>> on 28th March I sent a question about the general AMBER force field
>> (GAFF) to this mailing list, but nobody seems use it.
>> Does someone can tell me where I can get any answer?
>> I've already visited the GAFF page
>> <http://amber.scripps.edu/antechamber/gaff.html>.
>>
>> Regards,
>>
>> Eric.
>>
>>
>> --
>> / 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. /
>>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> http://www.eml-r.org
> ----------------------------------------------------------------------------
>
> 

-- 
/ 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