[gmx-users] Topology file of molecule
Krzysztof Kolman
krzysztof.kolman at gmail.com
Thu Nov 23 10:24:21 CET 2017
Dear Gromacs Users,
I would like to perform a simulation of adsorption of 3,4-Dihydroxybenzoic
acid (34DHBA) on silica surface using the OPLS-AA forcefield. I created
topology files for the silica surface based on the information found in
papers describing simulations of quartz (Wensink 2000
- 10.1021/la053284f, van der Spoel 2006 -10.1021/la053284f ). The topology
for 34DHBA was created using STaGE script (Lundborg 2015
- 10.1021/jp505332p) but some of the parameters (dihedrals) were missing
and GAFF parameters were used instead. Please find below the content of itp
file:
[ moleculetype ]
; Name nrexcl
34DHBA_opls 3
[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot
bond_type
1 opls_145 1 LIG C1 1 -0.115000 12.01100 ; -0.115000
CA
2 opls_166 1 LIG C2 2 0.150000 12.01100 ; 0.035000
CA
3 opls_166 1 LIG C3 3 0.150000 12.01100 ; 0.185000
CA
4 opls_145 1 LIG C4 4 -0.115000 12.01100 ; 0.070000
CA
5 opls_145 1 LIG C5 5 -0.115000 12.01100 ; -0.045000
CA
6 opls_145 1 LIG C6 6 -0.115000 12.01100 ; -0.160000
CA
7 opls_167 1 LIG OC3 7 -0.585000 15.99940 ; -0.745000
OH
8 opls_167 1 LIG OC2 8 -0.585000 15.99940 ; -1.330000
OH
9 opls_470 1 LIG C9 9 0.635000 12.01100 ; -0.695000
C
10 opls_269 1 LIG OC91 10 -0.440000 15.99940 ; -1.135000
O_3
11 opls_268 1 LIG OC92 11 -0.530000 15.99940 ; -1.665000
OH
12 opls_146 1 LIG HC1 12 0.115000 1.00800 ; -1.550000
HA
13 opls_146 1 LIG HC4 13 0.115000 1.00800 ; -1.435000
HA
14 opls_146 1 LIG HC6 14 0.115000 1.00800 ; -1.320000
HA
15 opls_168 1 LIG HO3 15 0.435000 1.00800 ; -0.885000
HO
16 opls_168 1 LIG HO2 16 0.435000 1.00800 ; -0.450000
HO
17 opls_270 1 LIG HO92 17 0.450000 1.00800 ; 0.000000
HO
[ bonds ]
; ai aj funct r k
1 2 1 1.4000e-01 3.9246e+05 ; CA - CA
1 6 1 1.4000e-01 3.9246e+05 ; CA - CA
1 12 1 1.0800e-01 3.0711e+05 ; CA - HA
2 3 1 1.4000e-01 3.9246e+05 ; CA - CA
2 8 1 1.3640e-01 3.7656e+05 ; CA - OH
3 4 1 1.4000e-01 3.9246e+05 ; CA - CA
3 7 1 1.3640e-01 3.7656e+05 ; CA - OH
4 5 1 1.4000e-01 3.9246e+05 ; CA - CA
4 13 1 1.0800e-01 3.0711e+05 ; CA - HA
5 6 1 1.4000e-01 3.9246e+05 ; CA - CA
5 9 1 1.4900e-01 3.3472e+05 ; CA - C
6 14 1 1.0800e-01 3.0711e+05 ; CA - HA
7 15 1 9.4500e-02 4.6275e+05 ; OH - HO
8 16 1 9.4500e-02 4.6275e+05 ; OH - HO
9 10 1 1.2290e-01 4.7698e+05 ; C - O_3
9 11 1 1.3640e-01 3.7656e+05 ; C - OH
11 17 1 9.4500e-02 4.6275e+05 ; OH - HO
[ pairs ]
; ai aj funct
1 4 1 ; C1 - C4
1 7 1 ; C1 - OC3
1 9 1 ; C1 - C9
1 16 1 ; C1 - HO2
2 5 1 ; C2 - C5
2 13 1 ; C2 - HC4
2 14 1 ; C2 - HC6
2 15 1 ; C2 - HO3
3 9 1 ; C3 - C9
3 16 1 ; C3 - HO2
4 8 1 ; C4 - OC2
4 10 1 ; C4 - OC91
4 11 1 ; C4 - OC92
4 14 1 ; C4 - HC6
4 15 1 ; C4 - HO3
5 7 1 ; C5 - OC3
5 17 1 ; C5 - HO92
6 3 1 ; C6 - C3
6 8 1 ; C6 - OC2
6 10 1 ; C6 - OC91
6 11 1 ; C6 - OC92
6 13 1 ; C6 - HC4
7 8 1 ; OC3 - OC2
7 13 1 ; OC3 - HC4
9 13 1 ; C9 - HC4
9 14 1 ; C9 - HC6
10 17 1 ; OC91 - HO92
12 3 1 ; HC1 - C3
12 5 1 ; HC1 - C5
12 8 1 ; HC1 - OC2
12 14 1 ; HC1 - HC6
[ angles ]
; ai aj ak funct theta cth
1 2 3 1 1.2000e+02 5.2718e+02 ; CA - CA - CA
1 2 8 1 1.2000e+02 5.8576e+02 ; CA - CA - OH
1 6 5 1 1.2000e+02 5.2718e+02 ; CA - CA - CA
1 6 14 1 1.2000e+02 2.9288e+02 ; CA - CA - HA
2 1 6 1 1.2000e+02 5.2718e+02 ; CA - CA - CA
2 1 12 1 1.2000e+02 2.9288e+02 ; CA - CA - HA
2 3 4 1 1.2000e+02 5.2718e+02 ; CA - CA - CA
2 3 7 1 1.2000e+02 5.8576e+02 ; CA - CA - OH
2 8 16 1 1.1300e+02 2.9288e+02 ; CA - OH - HO
3 2 8 1 1.2000e+02 5.8576e+02 ; CA - CA - OH
3 4 5 1 1.2000e+02 5.2718e+02 ; CA - CA - CA
3 4 13 1 1.2000e+02 2.9288e+02 ; CA - CA - HA
3 7 15 1 1.1300e+02 2.9288e+02 ; CA - OH - HO
4 3 7 1 1.2000e+02 5.8576e+02 ; CA - CA - OH
4 5 6 1 1.2000e+02 5.2718e+02 ; CA - CA - CA
4 5 9 1 1.2000e+02 7.1128e+02 ; CA - CA - C
5 4 13 1 1.2000e+02 2.9288e+02 ; CA - CA - HA
5 6 14 1 1.2000e+02 2.9288e+02 ; CA - CA - HA
5 9 10 1 1.2040e+02 6.6944e+02 ; CA - C - O_3
5 9 11 1 1.2000e+02 5.8576e+02 ; CA - C - OH
6 1 12 1 1.2000e+02 2.9288e+02 ; CA - CA - HA
6 5 9 1 1.2000e+02 7.1128e+02 ; CA - CA - C
9 11 17 1 1.1300e+02 2.9288e+02 ; C - OH - HO
10 9 11 1 1.2100e+02 6.6944e+02 ; O_3 - C - OH
[ dihedrals ] ; propers
; for gromacs 4.5 or higher, using funct 9
; i j k l func phase kd pn
1 2 3 4 9 180.00 15.16700 2 ; C1- C2-
C3- C4 !Warning using GAFF parameters!
1 2 3 7 9 180.00 15.16700 2 ; C1- C2-
C3- OC3 !Warning using GAFF parameters!
1 2 8 16 9 180.00 3.76560 2 ; C1- C2-
OC2- HO2 !Warning using GAFF parameters!
1 6 5 4 9 180.00 15.16700 2 ; C1- C6-
C5- C4 !Warning using GAFF parameters!
1 6 5 9 9 180.00 15.16700 2 ; C1- C6-
C5- C9 !Warning using GAFF parameters!
2 1 6 5 9 180.00 15.16700 2 ; C2- C1-
C6- C5 !Warning using GAFF parameters!
2 1 6 14 9 180.00 15.16700 2 ; C2- C1-
C6- HC6 !Warning using GAFF parameters!
2 3 4 5 9 180.00 15.16700 2 ; C2- C3-
C4- C5 !Warning using GAFF parameters!
2 3 4 13 9 180.00 15.16700 2 ; C2- C3-
C4- HC4 !Warning using GAFF parameters!
2 3 7 15 9 180.00 3.76560 2 ; C2- C3-
OC3- HO3 !Warning using GAFF parameters!
3 2 8 16 9 180.00 3.76560 2 ; C3- C2-
OC2- HO2 !Warning using GAFF parameters!
3 4 5 6 9 180.00 15.16700 2 ; C3- C4-
C5- C6 !Warning using GAFF parameters!
3 4 5 9 9 180.00 15.16700 2 ; C3- C4-
C5- C9 !Warning using GAFF parameters!
4 3 2 8 9 180.00 15.16700 2 ; C4- C3-
C2- OC2 !Warning using GAFF parameters!
4 3 7 15 9 180.00 3.76560 2 ; C4- C3-
OC3- HO3 !Warning using GAFF parameters!
4 5 6 14 9 180.00 15.16700 2 ; C4- C5-
C6- HC6 !Warning using GAFF parameters!
4 5 9 10 9 180.00 4.18400 2 ; C4- C5-
C9- OC91 !Warning using GAFF parameters!
4 5 9 11 9 180.00 4.18400 2 ; C4- C5-
C9- OC92 !Warning using GAFF parameters!
5 4 3 7 9 180.00 15.16700 2 ; C5- C4-
C3- OC3 !Warning using GAFF parameters!
5 9 11 17 9 180.00 9.62320 2 ; C5- C9-
OC92- HO92 !Warning using GAFF parameters!
6 1 2 3 9 180.00 15.16700 2 ; C6- C1-
C2- C3 !Warning using GAFF parameters!
6 1 2 8 9 180.00 15.16700 2 ; C6- C1-
C2- OC2 !Warning using GAFF parameters!
6 5 4 13 9 180.00 15.16700 2 ; C6- C5-
C4- HC4 !Warning using GAFF parameters!
6 5 9 10 9 180.00 4.18400 2 ; C6- C5-
C9- OC91 !Warning using GAFF parameters!
6 5 9 11 9 180.00 4.18400 2 ; C6- C5-
C9- OC92 !Warning using GAFF parameters!
7 3 2 8 9 180.00 15.16700 2 ; OC3- C3-
C2- OC2 !Warning using GAFF parameters!
7 3 4 13 9 180.00 15.16700 2 ; OC3- C3-
C4- HC4 !Warning using GAFF parameters!
9 5 4 13 9 180.00 15.16700 2 ; C9- C5-
C4- HC4 !Warning using GAFF parameters!
9 5 6 14 9 180.00 15.16700 2 ; C9- C5-
C6- HC6 !Warning using GAFF parameters!
10 9 11 17 9 0.00 7.94960 1 ; OC91- C9-
OC92- HO92 !Warning using GAFF parameters!
10 9 11 17 9 180.00 9.62320 2 ; OC91- C9-
OC92- HO92 !Warning using GAFF parameters!
12 1 2 3 9 180.00 15.16700 2 ; HC1- C1-
C2- C3 !Warning using GAFF parameters!
12 1 2 8 9 180.00 15.16700 2 ; HC1- C1-
C2- OC2 !Warning using GAFF parameters!
12 1 6 5 9 180.00 15.16700 2 ; HC1- C1-
C6- C5 !Warning using GAFF parameters!
12 1 6 14 9 180.00 15.16700 2 ; HC1- C1-
C6- HC6 !Warning using GAFF parameters!
[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
; i j k l func phase kd pn
1 3 2 8 4 180.00 4.60240 2 ; C1- C3-
C2- OC2 !Warning using GAFF parameters!
1 5 6 14 4 180.00 4.60240 2 ; C1- C5-
C6- HC6 !Warning using GAFF parameters!
2 4 3 7 4 180.00 4.60240 2 ; C2- C4-
C3- OC3 !Warning using GAFF parameters!
3 5 4 13 4 180.00 4.60240 2 ; C3- C5-
C4- HC4 !Warning using GAFF parameters!
5 10 9 11 4 180.00 43.93200 2 ; C5- OC91-
C9- OC92 !Warning using GAFF parameters!
9 4 5 6 4 180.00 4.60240 2 ; C9- C4-
C5- C6 !Warning using GAFF parameters!
12 1 6 2 4 180.00 4.60240 2 ; HC1- C1-
C6- C2 !Warning using GAFF parameters!
Generally one should not mix different forcefiedls but my question is how
big "mistake" I make running a simulation using the parameters shown above.
Is there any benchmark that allows to evaluate the quality of a topology
file (maybe by calculating some experimental properties)?
Thank you in advance for your help.
Best regards,
Krzysztof
More information about the gromacs.org_gmx-users
mailing list