[gmx-users] Including a solvation model after converting from AMBER to GROMACS
Massih Khorvash
massih.khorvash at gmail.com
Thu Jun 16 21:47:13 CEST 2011
Hello,
I first used Antechamber and Leap to generate the topology and coordinate
files for benzamide.pdb.
I then converted them to gromacs formats and added the water molecules using
the following commands:
editconf -f benz.gro -bt dodecahedron -d 1.2 -o benz_box.gro
genbox -cp benz_box.gro -cs tip4p.gro (there was no tip3p.gro) -p benz.top
-o benz_solvated.gro
*************************************************************
; benz.top created by rdparm2gmx.pl Wed Jun 8 14:58:07 MDT 2011
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon
n n 0.0000 0.0000 A 3.25000e-01 7.11280e-01
c c 0.0000 0.0000 A 3.39967e-01 3.59824e-01
ha ha 0.0000 0.0000 A 2.59964e-01 6.27600e-02
hn hn 0.0000 0.0000 A 1.06908e-01 6.56888e-02
ca ca 0.0000 0.0000 A 3.39967e-01 3.59824e-01
o o 0.0000 0.0000 A 2.95992e-01 8.78640e-01
[ moleculetype ]
; Name nrexcl
solute 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB
1 ca 1 MOL C 1 -0.07700 12.000000
2 ca 1 MOL C1 2 -0.13800 12.000000
3 ca 1 MOL C2 3 -0.10900 12.000000
4 ca 1 MOL C3 4 -0.13900 12.000000
5 ca 1 MOL C4 5 -0.10500 12.000000
6 ca 1 MOL C5 6 -0.14160 12.000000
7 c 1 MOL C6 7 0.67070 12.000000
8 o 1 MOL O 8 -0.61010 16.000000
9 n 1 MOL N 9 -0.67400 14.000000
10 ha 1 MOL H 10 0.15600 1.000000
11 ha 1 MOL H1 11 0.13800 1.000000
12 ha 1 MOL H2 12 0.13500 1.000000
13 ha 1 MOL H3 13 0.13600 1.000000
14 ha 1 MOL H4 14 0.13300 1.000000
15 hn 1 MOL H5 15 0.31750 1.000000
16 hn 1 MOL H6 16 0.30750 1.000000
[ bonds ]
; ai aj funct r k
1 10 1 1.0870e-01 2.8811e+05
2 11 1 1.0870e-01 2.8811e+05
3 12 1 1.0870e-01 2.8811e+05
4 13 1 1.0870e-01 2.8811e+05
5 14 1 1.0870e-01 2.8811e+05
9 15 1 1.0090e-01 3.4326e+05
9 16 1 1.0090e-01 3.4326e+05
1 2 1 1.3870e-01 4.0033e+05
1 6 1 1.3870e-01 4.0033e+05
2 3 1 1.3870e-01 4.0033e+05
3 4 1 1.3870e-01 4.0033e+05
4 5 1 1.3870e-01 4.0033e+05
5 6 1 1.3870e-01 4.0033e+05
6 7 1 1.4870e-01 2.9263e+05
7 8 1 1.2140e-01 5.4225e+05
7 9 1 1.3450e-01 4.0016e+05
[ pairs ]
; ai aj funct
1 12 1
1 14 1
2 13 1
10 3 1
3 14 1
4 11 1
5 12 1
10 5 1
6 11 1
6 13 1
6 15 1
6 16 1
10 7 1
7 14 1
8 15 1
8 16 1
10 11 1
11 12 1
12 13 1
13 14 1
1 4 1
1 8 1
1 9 1
2 5 1
2 7 1
6 3 1
4 7 1
5 8 1
5 9 1
[ angles ]
; ai aj ak funct theta cth
1 2 11 1 1.2001e+02 4.0551e+02
2 1 10 1 1.2001e+02 4.0551e+02
2 3 12 1 1.2001e+02 4.0551e+02
3 2 11 1 1.2001e+02 4.0551e+02
3 4 13 1 1.2001e+02 4.0551e+02
4 3 12 1 1.2001e+02 4.0551e+02
4 5 14 1 1.2001e+02 4.0551e+02
5 4 13 1 1.2001e+02 4.0551e+02
6 1 10 1 1.2001e+02 4.0551e+02
6 5 14 1 1.2001e+02 4.0551e+02
7 9 15 1 1.1846e+02 4.1179e+02
7 9 16 1 1.1846e+02 4.1179e+02
15 9 16 1 1.1785e+02 3.3246e+02
1 2 3 1 1.1997e+02 5.6216e+02
1 6 5 1 1.1997e+02 5.6216e+02
1 6 7 1 1.2014e+02 5.4091e+02
2 1 6 1 1.1997e+02 5.6216e+02
2 3 4 1 1.1997e+02 5.6216e+02
3 4 5 1 1.1997e+02 5.6216e+02
4 5 6 1 1.1997e+02 5.6216e+02
5 6 7 1 1.2014e+02 5.4091e+02
6 7 8 1 1.2344e+02 5.7463e+02
6 7 9 1 1.1514e+02 5.7296e+02
8 7 9 1 1.2203e+02 6.3455e+02
[ dihedrals ]
;i j k l func C0 ... C5
1 2 3 12 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
1 6 5 14 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
2 3 4 13 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
10 1 2 3 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
3 4 5 14 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
4 3 2 11 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
5 4 3 12 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
10 1 6 5 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
6 1 2 11 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
6 5 4 13 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
6 7 9 15 3 20.92000 0.00000 -20.92000
0.00000 0.00000 0.00000 ;
6 7 9 16 3 20.92000 0.00000 -20.92000
0.00000 0.00000 0.00000 ;
10 1 6 7 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
7 6 5 14 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
8 7 9 15 3 29.28800 -8.36800 -20.92000
0.00000 0.00000 0.00000 ;
8 7 9 16 3 29.28800 -8.36800 -20.92000
0.00000 0.00000 0.00000 ;
10 1 2 11 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
11 2 3 12 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
12 3 4 13 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
13 4 5 14 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
10 1 6 2 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
1 3 2 11 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
2 4 3 12 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
3 5 4 13 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
4 6 5 14 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
7 15 9 16 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
1 2 3 4 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
1 6 5 4 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
1 6 7 8 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
1 6 7 9 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
2 1 6 5 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
2 1 6 7 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
2 3 4 5 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
6 1 2 3 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
3 4 5 6 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
4 5 6 7 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
5 6 7 8 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
5 6 7 9 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
6 9 7 8 3 87.86400 0.00000 -87.86400
0.00000 0.00000 0.00000 ;
[ system ]
16 system in water
[ molecules ]
; Compound nmols
solute 1
SOL 697
*******************************************************************************************
When I try to run the minimizer, I get this error:
Fatal error:
No such moleculetype SOL
****************************************************************
I added this line to benz.top file:
*#include "amber99.ff/tip4p.itp"*
[ system ]
16 system in water
I get this error when minimizing:
Fatal error:
Atomtype OW_tip4p not found
Thanks
Massih
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