Hi Not because I developed ACPYPE, but if I’d like to be the most rigorous as possible, I’d go with ACPYPE and RED (http://q4md-forcefieldtools.org/).
Alan On 29 May 2015 at 20:53, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > I continued to define good partial charges using the tools suggested. I > found that the combination of Maestro + ffconv or mktop, ACPYPE and > antechamber + mktop have all advantages and disadvantages depending on the > organic molecule. > > for instance for acetone with maestro and mktop i could achieve the same > topology as virtual chemistry. I next tried to generate a topology for > iso-propanol. Here ACPYPE charges with the mktop atom types gave the closes > density to the experimental one. I also tried to calculate the heat > capacity with Cp and Cv to compare it with the literature. My box is > 2.3x2.3x2.3nm large and has about 150 molecules of the organic solvent. > After 1ns of NPT i get values which are 5x higher than the literature value > (gmx energy -f npt.edr -fluct_props -nmol 100). I also tried a box 5x5x5nm > with over 1000 molecules and got the same result. Any idea why the > simulation using OPLS AA FF is so far of when it comes to the heat capacity? > > thanks > max > > > > > On May 28, 2015, at 9:19 AM, Ebert Maximilian <m.eb...@umontreal.ca> > wrote: > > > > 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.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? 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. > >>> > >>> > >>> -- > >>> 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. > >>> > >> -- > >> 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. > > > > -- > > 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. > > -- > 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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