[gmx-users] Simulation with nbutanol
Juliana Angeiras
juangeiras at yahoo.com.br
Tue Apr 24 03:47:22 CEST 2012
Hello,
I'm trying to build a box with nbutanol using the residue below for nbutanol (But), added in ffoplsaa.rtp
; Butanol
[ But ]
[ atoms ]
;
C1 opls_135 -0.18 1
H11 opls_140 0.06 1
H12 opls_140 0.06 1
H13 opls_140 0.06 1
C2 opls_136 -0.12 2
H21 opls_140 0.06 2
H22 opls_140 0.06 2
C3 opls_136 -0.12 3
H31 opls_140 0.06 3
H32 opls_140 0.06 3
C4 opls_157 0.145 4
H41 opls_140 0.06 4
H42 opls_140 0.06 4
OH opls_154 -0.683 4
HO opls_155 0.418 4
[ bonds ]
; ai aj funct c0 c1 c2 c3
C1 H11
C1 H12
C1 H13
C1 C2
C2 H21
C2 H22
C2 C3
C3 H31
C3 H32
C3 C4
C4 H41
C4 H42
C4 OH
OH HO
[ angles ]
; ai aj ak funct c0 c1 c2 c3
H11 C1 H12
H11 C1 H13
H11 C1 C2
H12 C1 H13
H12 C1 C2
H13 C1 C2
C1 C2 H21
C1 C2 H22
C1 C2 C3
H21 C2 H22
H21 C2 C3
H22 C2 C3
C2 C3 H31
C2 C3 H32
C2 C3 C4
H31 C3 H32
H31 C3 C4
H32 C3 C4
C3 C4 H41
C3 C4 H42
C3 C4 OH
H41 C4 H42
H41 C4 OH
H42 C4 OH
C4 OH HO
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
H11 C1 C2 H21
H11 C1 C2 H22
H11 C1 C2 C3
H12 C1 C2 H21
H12 C1 C2 H22
H12 C1 C2 C3
H13 C1 C2 H21
H13 C1 C2 H22
H13 C1 C2 C3
C1 C2 C3 H31
C1 C2 C3 H32
C1 C2 C3 C4
H21 C2 C3 H31
H21 C2 C3 H32
H21 C2 C3 C4
H22 C2 C3 H31
H22 C2 C3 H32
H22 C2 C3 C4
C2 C3 C4 H41
C2 C3 C4 H42
C2 C3 C4 OH
H31 C3 C4 H41
H31 C3 C4 H42
H31 C3 C4 OH
H32 C3 C4 H41
H32 C3 C4 H42
H32 C3 C4 OH
C3 C4 OH HO
H41 C4 OH HO
H42 C4 OH HO
The .gro file used is
15
1But C1 1 2.561 2.686 0.006
1But H11 2 2.470 2.721 -0.042
1But H12 3 2.576 2.582 -0.021
1But H13 4 2.544 2.690 0.114
1But C2 5 2.681 2.772 -0.034
1But H21 6 2.692 2.769 -0.143
1But H22 7 2.661 2.877 -0.008
1But C3 8 2.811 2.727 0.033
1But H31 9 2.799 2.730 0.141
1But H32 10 2.831 2.623 0.007
1But C4 11 2.932 2.813 -0.008
1But H41 12 2.947 2.810 -0.116
1But H42 13 2.916 2.917 0.020
1But OH 14 3.048 2.765 0.055
1But HO 15 3.122 2.816 0.026
2.75000 2.75000 2.75000
The command line for obtaining the topology file:
pdb2gmx -f nbutoh.gro -o nbutoh2.gro -p topol.top
return the error message:
Fatal error:
Invalid line in nbutoh.gro for atom 1:
1But C1 1 2.561 2.686 0.006
I have tried of different ways for obtaining the gro and the topology file, include using the pdb file below, butit still fails.
HETATM 1 C1 But 1 2.510 -0.293 0.000
HETATM 2 H11 But 1 3.385 0.351 -0.000
HETATM 3 H12 But 1 2.567 -0.931 0.878
HETATM 4 H13 But 1 2.567 -0.931 -0.878
HETATM 5 C2 But 1 1.222 0.528 -0.000
HETATM 6 H21 But 1 1.212 1.180 0.871
HETATM 7 H22 But 1 1.212 1.180 -0.871
HETATM 8 C3 But 1 -0.036 -0.341 -0.000
HETATM 9 H31 But 1 -0.041 -0.990 -0.873
HETATM 10 H32 But 1 -0.041 -0.990 0.873
HETATM 11 C4 But 1 -1.317 0.471 0.000
HETATM 12 H41 But 1 -1.349 1.113 0.880
HETATM 13 H42 But 1 -1.349 1.113 -0.880
HETATM 14 OH But 1 -2.404 -0.419 0.000
HETATM 15 HO Bu t 1 -3.209 0.066 0.000
CONECT 1 2 3 4 5
CONECT 2 1
CONECT 3 1
CONECT 4 1
CONECT 5 1 6 7 8
CONECT 6 5
CONECT 7 5
CONECT 8 5 9 10 11
CONECT 9 8
CONECT 10 8
CONECT 11 8 12 13 14
CONECT 12 11
CONECT 13 11
CONECT 14 11 15
CONECT 15 14
END
Can you help me to solve my problem?
Thanks,
--
Juliana Angeiras Batista da Silva
Laboratório de Química Teórica e Computacional
Departamento de Química Fundamental
Universidade Federal de Pernambuco
50740-540 Recife (PE) - Brazil
Phone: +55 81 2126-8440 ext. 5007
Phone: +55 81 9197-9297.
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