[gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
Kalev Takkis
kalev.takkis at gmail.com
Thu May 28 08:22:50 CEST 2015
If you're after OPLS topologies for GROMACS then one way to derive them is
via Schrödinger's Maestro (free academics version is sufficient) and
Andrey Frolov's
ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can
create a force field represesentation of a molecule with the former
(described here http://www.schrodinger.com/kb/809) and then convert it to
GROMACS format with the latter.
All the best,
Kalev
On 28 May 2015 at 03:37, Mohd Farid Ismail <mohd.farid.ismail at yandex.com>
wrote:
> You can try R.E.D. Server. It has more charge models (I don't know
> whether that will help).
>
> Also, IMO, one should target the density and the static dielectric
> constant when it comes to VDW and partial charges. I saw a recent paper
> that might be of interest to you
> http://pubs.acs.org/doi/abs/10.1021/jp3002383
>
> --
> Mohd Farid Ismail
>
>
>
>
> 28.05.2015, 05:13, "Ebert Maximilian" <m.ebert at umontreal.ca>:
>
> I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with
> acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For
> the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2
> value on their website) and for the parameter derived as explain in
> previous mail I got 817.0 which seems too high. Does anybody has an advice
> how I could improve the derivation of my parameters?
>
> Thank you very much,
>
> max
>
> On May 27, 2015, at 3:25 PM, Ebert Maximilian <m.ebert at umontreal.ca>
> wrote:
>
> I read more about organic solvents in MD and came to the conclusion that
> OPLS is indeed the best way to go. Since I couldn’t really find an
> accessible tutorial how to derive topology files for GROMACS and the FF
> OPLS/AA I will document my progress here. Maybe this is of help for
> somebody in the future. In addition, I would like to ask the community to
> help me in case you see problems with my approach. Once I have a good
> protocol I will write a tutorial and make it available online.
>
> To validate my approach I am trying to create a parameter set for acetone
> which I found on http://virtualchemistry.org. To generate the OPLS
> topology I used a tool suggested by many people called mktop in version
> 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and
> generated a GROMACS topology file using the following command:
>
> mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes
>
> In order to get the charges for this organic molecule I downloaded the
> most recent amber tools and compiled it. I used the AM1-BCC charge model to
> generate charges for acetone using the following instructions in
> antechamber:
>
> antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2
>
> I opened the resulting mol2 file in Chimera to map the atoms to the atoms
> in my .top file. The charges calculated by antechamber look reasonable and
> are comparable to the validated OPLS topology from virtual chemistry:
>
> virtual chemistry charges
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 opls_280 1 LIG C 1 0.47
> 12.011
> 2 opls_135 1 LIG C 2 -0.18
> 12.011
> 3 opls_135 1 LIG C 3 -0.18
> 12.011
> 4 opls_281 1 LIG O 4 -0.47
> 15.9994
> 5 opls_282 1 LIG H 5 0.06
> 1.008
> 6 opls_282 1 LIG H 6 0.06
> 1.008
> 7 opls_282 1 LIG H 7 0.06
> 1.008
> 8 opls_282 1 LIG H 8 0.06
> 1.008
> 9 opls_282 1 LIG H 9 0.06
> 1.008
> 10 opls_282 1 LIG H 10 0.06
> 1.008
>
>
> antechamber AM1-BCC derived
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 opls_280 1 ACN C1 1 0.56 12.011
> 2 opls_281 1 ACN O1 1 -0.52 15.9994
> 3 opls_135 1 ACN C2 2 -0.20 12.011
> 4 opls_135 1 ACN C3 3 -0.20 12.011
> 5 opls_282 1 ACN H1 2 0.06 1.008
> 6 opls_282 1 ACN H2 2 0.06 1.008
> 7 opls_282 1 ACN H3 2 0.06 1.008
> 8 opls_282 1 ACN H4 3 0.06 1.008
> 9 opls_282 1 ACN H5 3 0.06 1.008
> 10 opls_282 1 ACN H6 3 0.06 1.008
>
> The atom types were guessed correctly by mktop and also the charge groups
> make sense I think. So far so good.
>
> I realize some differences between the two topologies. First the mktop
> topology also includes FF constants for the different bonds and angles:
>
> [ bonds ]
> 1 2 1 0.121 476976.0
> 1 3 1 0.151 265265.6
> 1 4 1 0.151 265265.6
> 3 5 1 0.109 284512.0
> 3 6 1 0.109 284512.0
> 3 7 1 0.109 284512.0
> 4 8 1 0.109 284512.0
> 4 9 1 0.109 284512.0
> 4 10 1 0.109 284512.0
>
>
> [ angles ]
> 1 3 5 1 109.460 292.880
> 1 3 6 1 109.473 292.880
> 1 3 7 1 109.484 292.880
> 1 4 8 1 109.466 292.880
> 1 4 9 1 109.435 292.880
> 1 4 10 1 109.477 292.880
> 2 1 3 1 119.985 669.440
> 2 1 4 1 119.985 669.440
> 3 1 4 1 120.029 585.760
> 5 3 6 1 109.445 276.144
> 5 3 7 1 109.464 276.144
> 6 3 7 1 109.502 276.144
> 8 4 9 1 109.483 276.144
> 8 4 10 1 109.504 276.144
> 9 4 10 1 109.462 276.144
>
> compared to the virtual chemistry file:
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 3 1
> 1 4 1
> 2 5 1
> 2 6 1
> 2 7 1
> 3 8 1
> 3 9 1
> 3 10 1
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2
> c3
> 2 1 3 1
> 2 1 4 1
> 3 1 4 1
> 1 2 5 1
> 1 2 6 1
> 1 2 7 1
> 5 2 6 1
> 5 2 7 1
> 6 2 7 1
> 1 3 8 1
> 1 3 9 1
> 1 3 10 1
> 8 3 9 1
> 8 3 10 1
> 9 3 10 1
>
>
> Should I trust the mktop parameters or delete them? To look if my
> parameters are correct I did a short MD with a box containing only acetone
> based on the two topologies. The MD is still running but I wanted to
> compare the density and see how it matches with reality.
>
> What do you think about this approach? What would have been a better way?
> How can I make sure that the charges are correct?
>
> Thanks for your input.
>
> Max
>
>
>
> On May 27, 2015, at 11:54 AM, Ebert Maximilian <m.ebert at umontreal.ca
> <mailto:m.ebert at umontreal.ca>> wrote:
>
> Hi there,
>
> I am about to setup a water:organic solvent mixture with a protein. I
> found many organic molecules on http://virtualchemistry.org with
> definitions for the OPLS FF. However, some are missing so I would need to
> derive the parameters myself. Before going into more details I was
> wondering if OPLS is to be preferred if organic solvent is present or can
> AMBER also be used? It seems that using ACPYPE with AMBER is much more
> accessible than using any other method to derive the parameters for organic
> molecules.
>
> Thanks for your advice.
> --
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