[gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
Ebert Maximilian
m.ebert at umontreal.ca
Mon Jun 1 18:02:58 CEST 2015
Hi,
thanks diana for your input and for the review. I never used GROMOS so far and I feel less comfortable using an unknown FF at this point. I am writing a tutorial on how to parameterize organic molecules right now and will publish it this week. Maybe you can comment on the strategy to have a relatively clean and broad approach. I was wondering which physical-chemical properties did you use to verify your definition? So far I am looking at density, Cp and Cv.
Thanks!
Max
> On May 28, 2015, at 5:15 AM, Diana Lousa <dlousa at itqb.unl.pt> wrote:
>
> 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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> Gromacs Users mailing list
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