Dear justin here it is .the files is attached.I insert gd-29 in line before the last line (dehidral) so . best -- sh-karbalaee
; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Aug 21 23:30:46 2008 ; ; This is your topology file ; "Disturb the Peace of a John Q Citizen" (Urban Dance Squad) ; ; Include forcefield parameters #include "ffG53a5.itp"
[ moleculetype ]
; Name nrexcl
TFE 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 H 1 TFE HT 1 0.41 1.008 ; qtot
0.41
2 OTFE 1 TFE OT 1 -0.625 15.9994 ; qtot
-0.215
3 CHTFE 1 TFE CH2T 1 0.273 14.027 ; qtot
0.058
4 CTFE 1 TFE CT 1 0.452 12.011 ; qtot
0.51
5 FTFE 1 TFE F1T 1 -0.17 18.9984 ; qtot
0.34
6 FTFE 1 TFE F2T 1 -0.17 18.9984 ; qtot
0.17
7 FTFE 1 TFE F3T 1 -0.17 18.9984 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_1
2 3 2 gb_18
3 4 2 gb_27
4 5 2 gb_13
4 6 2 gb_13
4 7 2 gb_13
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
2 5 1
2 6 1
2 7 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 2 ga_50
2 3 4 2 ga_51
3 4 5 2 ga_52
3 4 6 2 ga_52
3 4 7 2 ga_52
5 4 6 2 ga_49
5 4 7 2 ga_49
6 4 7 2 ga_49
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
1 2 3 4 1 gd_24
2 3 4 5 1 gd_24
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "spce.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
TFE IN WATER in water
[ molecules ]
; Compound #mols
TFE 1
SOL 5866
tfe.itp
Description: Binary data
1vm52.top
Description: Binary data
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