[gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
Ebert Maximilian
m.ebert at umontreal.ca
Thu May 28 15:19:36 CEST 2015
Thanks Justin and Kalev this brings me already much further. I tried ffld_server and it works just fine. However, it is like a black box. I can’t really find the documentation on how ffld_server gets the charges. Do you know where to find the documentation?
Thanks
> On May 28, 2015, at 2:22 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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