[gmx-users] Topology file of molecule
Magnus Lundborg
magnus.lundborg at scilifelab.se
Thu Nov 23 13:51:51 CET 2017
Dear Krzysztof,
I wouldn't be too worried about the fact that GAFF parameters have been
used for proper and improper torsion angles. It happens quite a lot with
the OPLS-AA forcefield. But as always, it is good to verify that the
topology behaves as expected. Unfortunately there is no objective way to
do this. If there are no experimentally measured properties available of
your molecule it is a bit risky to proceed. However, I would recommend
running short simulations of the molecule in vacuum (NVT) and in a
simulation box solvated by itself just to see that it does at least not
behave very strangely. If it seems OK I think you can proceed with your
studies, but as always with an eye open for strange behaviour.
I hope that helps you.
Best regards,
Magnus
On 2017-11-23 10:24, Krzysztof Kolman wrote:
> 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
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