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From: Eric Germaneau <eric.germaneau.epfl.ch>

Date: Fri, 28 Mar 2008 13:38:41 +0100

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 ) ?

I thank you in advance,

Regards,

Eric.

Date: Fri, 28 Mar 2008 13:38:41 +0100

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 ) ?

I thank you in advance,

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.epfl.ch <mailto:eric.germaneau.epfl.ch> /Tel./: +41 (0)21 / 693 06 36 /Fax./: +41 (0)21 / 693 05 04 /msn/: aihaike.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.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Fri Apr 18 2008 - 21:14:45 PDT

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