[gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
Diana Lousa
dlousa at itqb.unl.pt
Thu May 28 11:15:12 CEST 2015
Hi,
Our group has done many studies using enzymes in organic solvents (with
different amounts of water) and we always used the GROMOS FF for the
proteins and compatible parameters for the solvents. We can find a review
of enzyme simulations in nonaqueous solvents here:
http://pubs.rsc.org/en/Content/ArticleLanding/2013/CP/c3cp51761f#!divAbstract
The parameters that we used for different solvents were able to reproduce
their physical-chemical properties. I can also tell you that from our
experience the latest GROMOS FF are able to reproduce the structural
properties of small peptides and proteins also seem to be quite stable when
these FF are used. Thus, using GROMOS 54A7 for the protein and compatible
parameters for organic solvents can be a good choice. However, if you want
to use PME for long-range electrostatics, you have to test if these
parameters work in these conditions, because they were developed to be used
with RF.
On Thu, May 28, 2015 at 7:22 AM, Kalev Takkis <kalev.takkis at gmail.com>
wrote:
> 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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--
Diana Lousa
Post-doc
Protein Modeling Laboratory
ITQB/UNL
Oeiras, Portugal
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