Hi,
On Aug 3, 2006, at 1:51 PM, Eudes Fileti wrote:
Dear Gmx users:
I am a new user and I have some questions
Somebody could say me what it means the index at atoms in the
ffoplsaabon.itp file (a fragment of file
is gave bellow).
Some are obvious (OH, is oxygen bonden to hydrogen and HO is a
hydrogen bonded to oxygen)
but definitively I dont know what type of bond makes the carbon
atoms like C_2, C_3 or C *.
I cant find this issue at manual so forgive me for the basic question.
They are just names, and thus not further explained in the manual :-)
The early versions of OPLS started from the Amber bonded terms and
then recalculated nonbonded interactions, charges, and torsions.
As the force field has evolved, such that e.g. carbon atoms that
previously had identical interactions ("C") now differ in some cases,
particularly torsions.
Since we use the bonded atom types to specify the torsion, we need to
use different names for them. So, C_1 through C_4 are essentially
variants of C.
Cheers,
Erik
Thank you
eef
; Some esoteric OPLS atomtypes are not freely available (or
depreciated).
; Interaction types involving these have been commented out.
[ bondtypes ]
; i j func b0 kb
OW HW 1 0.09572 502080.0 ; For TIP4F Water - wlj 1/98
OW LP 1 0.01750 753120.0 ; -idem-
C* HC 1 0.10800 284512.0 ;
C C3 1 0.15220 265265.6 ; END
C_2 C3 1 0.15220 265265.6 ; END
C_3 C3 1 0.15220 265265.6 ; END
C CA 1 0.14900 334720.0 ; wlj 8/97
C_2 CA 1 0.14900 334720.0 ; wlj 8/97
C_3 CA 1 0.14900 334720.0 ; wlj 8/97
C CB 1 0.14190 374049.6 ; GUA
C_2 CB 1 0.14190 374049.6 ; GUA
C_3 CB 1 0.14190 374049.6 ; GUA
C CM 1 0.14440 343088.0 ; THY
C_2 CM 1 0.14440 343088.0 ; THY
C_3 CM 1 0.14440 343088.0 ; THY
C CS 1 0.14900 334720.0 ;
C_2 CS 1 0.14900 334720.0 ;
C_3 CS 1 0.14900 334720.0 ;
C CT 1 0.15220 265265.6 ;
C_2 CT 1 0.15220 265265.6 ;
C_3 CT 1 0.15220 265265.6 ;
C CT_2 1 0.15220 265265.6 ; AA Calpha
C_3 CT_2 1 0.15220 265265.6 ; AA C-term
NO ON 1 0.12250 460240.0 ; wlj nitro
CS CW 1 0.13670 456892.8 ; wj/nm
CS CS 1 0.14240 392459.2 ; -idem-
CS CB 1 0.14240 392459.2 ; -idem-
CS HA 1 0.10800 307105.6 ; -idem-
CU NB 1 0.13200 343088.0 ; -idem-
CU CA 1 0.14210 392459.2 ; -idem-
CU HA 1 0.10800 307105.6 ; -idem-
NA NB 1 0.13490 334720.0 ; -idem-
OS NB 1 0.13990 386601.6 ; -idem-
OS CR 1 0.13570 386601.6 ; -idem-
C3 C3 1 0.15260 217568.0 ; Ethane
C! C! 1 0.14600 322168.0 ; wlj
C! CS 1 0.14600 322168.0 ; wlj
______________________________________
Eudes Eterno Fileti
Centro de Ciência Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166
CEP 09210-170
skype: eefileti
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