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.
