[gmx-users] Topology file of molecule
Krzysztof Kolman
krzysztof.kolman at gmail.com
Mon Dec 4 11:31:37 CET 2017
Dear Justin,
Since you last answer, I have been trying to find some description how to
perform dihedrals scans using some QM software and Gromacs. I have found
out that it used to be some QM software implemented in Gromacs (Orca) but
this implementation is not developed anymore and it does not work with
newer version of Gromacs and Orca, please correct me here if I am wrong. I
have been also trying to find out how to do the MM part using Gromacs and I
found out that the simulations should have some unusual parameters
(cutoffs, etc.) and it is quite tedious work since all the input files need
to be manually prepared. My question is do you know maybe if there is
somewhere a tutorial how to perform such scans using Gromacs where all this
knowledge is combined and also some semi-automatic solution is presented?
Best 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
>
> ==================================================
>
>
> --
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