[gmx-users] Topology file of molecule
Krzysztof Kolman
krzysztof.kolman at gmail.com
Fri Nov 24 09:12:29 CET 2017
Dear Magnus and Justin,
Thank you very much for your help.
Kind regards,
Krzysztof
2017-11-23 13:55 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 11/23/17 7:51 AM, Magnus Lundborg wrote:
>
>> 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.
>>
>>
> The rigorous test is to perform a QM energy scan over the dihedral. Rotate
> in increments of 15 degrees, optimize, and calculate the energy. This gives
> you a one-dimensional potential energy surface. Do the corresponding MM
> evaluations with the force field (in vacuo) and verify that the positions
> and magnitudes of the minima are comparable. If they're not, you need to do
> some refinement of the parameters. Otherwise it is extremely hard to define
> what "strange" is in a simulation; you don't know what the molecule should
> be doing in the first place.
>
> -Justin
>
>
> 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
>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list