AMBER Archive (2008)

Subject: Re: AMBER: GAFF

From: Eric Germaneau (eric.germaneau_at_epfl.ch)
Date: Fri Apr 04 2008 - 09:10:31 CDT

I'm agree with you but information about file formats, and what various
columns mean, is given in the "file formats
<http://amber.scripps.edu/formats.html#parm.dat>" link at the Amber web
page but it doesn't fit the GAFF function form
<http://amber.scripps.edu/antechamber/gaff.html#function>. I'm a
beginner in AMBER, after read documentations I've still some questions.

                                                                      
---------------------------------------------

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.

    * 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 part,

    * What is the expression of the improper potential in AMBER?

 From amber files format
<http://amber.scripps.edu/formats.html#parm.dat> 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, A_i
and B_i.

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

Many thanks !!

Vlad Cojocaru wrote:
> Dear Eric,
>
> gaff.dat should have exactly the same format as the parm9X.dat
> ....Gaff is just a generalization of the AMBER force field to better
> represent the molecular variety in the organic chemistry space (AMBER
> was developed mainly for biomolecules)
>
> So, everything that is written in the amber manual about the format of
> parmXX.dat should apply to gaff.dat ...(And as far as I recall the
> parm9X.dat files also have only 3 columns in the section on "impropers"
>
> Please somebody correct me if I am wrong here.
>
> Best wishes
> vlad
>
> Eric Germaneau wrote:
>> 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. /
>>
>
> --
> ----------------------------------------------------------------------------
> 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. /

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