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 <dlo...@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.tak...@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.ism...@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.eb...@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.eb...@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.eb...@umontreal.ca >>> <mailto:m.eb...@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. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org<mailto: >>> gmx-users-requ...@gromacs.org>. >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? 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Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > > > -- > Diana Lousa > Post-doc > Protein Modeling Laboratory > ITQB/UNL > Oeiras, Portugal > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? 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