Custom Search
-- Amy He Hadad Lab @ OSU He.1768.osu.edu From: Jones de Andrade via AMBER <amber.ambermd.org> Date: Thursday, February 15, 2024 at 12:03 PM To: AMBER Mailing List <amber.ambermd.org> Subject: Re: [AMBER] Dihedral Parametrization in Amber19: Same QM level as for 94? Hi Dr. Simmerling. Thanks for the prompt answer (and sorry for any mistyping: using the phone since we got our optical link severed here at university). Yes, that is what I called "traditional" protocol. My point is that this is the reported protocol for the original amber ff94/96 (only difference is that instead of fitting it would mostly focus on just the overall rotation energy barrier), and I even think it is the parametrization technique used for gaff, but it still managed no stablish the parameters of a X-CA-CA-X dihedral torsion (basically, a benzene ring). It always bothered me how it could actually be done on that way for such aromatic atoms for the same concern you expressed: the energy would skyrocket. So, how was the original X-CA-CA-X dihedral torsion force constant parametrized for ff94/96? Does anybody has any idea? Thanks a lot again, and best regards, Jones Em 15 de fevereiro de 2024 13:39:42 BRT, Carlos Simmerling <carlos.simmerling.stonybrook.edu> escreveu: >Hi Jones, >not sure I'm following you. In many fitting protocols, one rotates around >the bond of interest and calculates energy using QM or other reference >method, and then does the same in MM, then fits parameters to minimize the >difference. Are you asking how this is done for something like a double >bond? the energy would be much higher, and for benzene likely impractical >due to the coupling with bonds in the ring. but ethene can be done, and the >barrier calculate from the 90 deg geometry. >is that what you were asking? > > >On Thu, Feb 15, 2024 at 7:58 AM Jones de Andrade via AMBER < >amber.ambermd.org> wrote: > >> Hi Dr. Simmerling. >> >> First of all, yes, I'm sorry, I was meaning the ff19sb force field. >> >> And thanks for the clarification: the QM calculation level for the >> dihedral torsions indeed changed *a lot* through time. ff19sb is proof of >> that, and its paper kind of its testimony. ;) >> >> One additional question that concerns the "traditional" (lowest and >> highest energy conformations in a torsion rotation) torsions >> paranetrizatioms that is present at least in ff94/96, but I think still >> works at least in gaff: while in free rotating bonds it is simple to find >> and study those (two) conformations, on the opposite case it is sometimes >> hard to even picture it. I mean, how are/were the maximum energy dihedral >> torsions calculated for ethene, or even worst for a X-CA-CA-X dihedral? >> With 90º distorted ethene and benzene molecules? >> >> Thanks a lot for all help, >> >> Best regards, >> >> Jones >> >> Em 14 de fevereiro de 2024 09:00:52 BRT, Carlos Simmerling < >> carlos.simmerling.gmail.com> escreveu: >> >There are a variety of force fields and also training strategies. I am not >> >sure what you mean by "AMBER19". Amber itself is the software, and the >> >force fields have different names. If you mean the protein ff19sb force >> >field, I suggest reading the original article for details on the QM level >> >for training dihedrals (which included aqueous solvation). Others, such as >> >GAFF for small molecules, differ. >> > >> >On Tue, Feb 13, 2024, 10:02 PM Jones De Andrade via AMBER < >> amber.ambermd.org> >> >wrote: >> > >> >> Hi all. >> >> >> >> I' looking for an answer that will probably quite straightforward here. >> >> ;) >> >> >> >> I'm performing the parametrization of some dihedral torsions. I know >> >> from older amber versions and its papers (i.e, Cornell JACS 1995 and Fox >> >> JPCB 1998) that it used to be done at MP2/6-31G*//HF/6-31G* level. >> >> >> >> However, since Amber94/96 a lot of evolution happened until AMBER19, so >> >> I want to ask if there was any changes (possible improvements) on the >> >> "protocol" concerning *especifically* dihedrals torsions >> >> parametrization, or it it is still maintained at the same level. >> >> >> >> Thanks a lot in advance, >> >> >> >> Best regards, >> >> >> >> Jones >> >> -- >> >> Jones de Andrade >> >> (jdandrade.iq.ufrgs.br) >> >> DFQ/IQ/UFRGS >> >> Lattes: https://urldefense.com/v3/__http://lattes.cnpq.br/6675936210583999__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua62p5Mjyt8$<https://urldefense.com/v3/__http:/lattes.cnpq.br/6675936210583999__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua62p5Mjyt8$> >> >> Orcid: https://urldefense.com/v3/__https://orcid.org/0000-0003-3429-8119__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua62JhFJEG4$<https://urldefense.com/v3/__https:/orcid.org/0000-0003-3429-8119__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua62JhFJEG4$> >> >> ResearcherID: https://urldefense.com/v3/__https://publons.com/researcher/AAC-5337-2019/__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua622AyCUgI$<https://urldefense.com/v3/__https:/publons.com/researcher/AAC-5337-2019/__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua622AyCUgI$> >> >> >> >> _______________________________________________ >> >> AMBER mailing list >> >> AMBER.ambermd.org >> >> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua628U3io3o$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua628U3io3o$> >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua628U3io3o$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua628U3io3o$> >> _______________________________________________ AMBER mailing list AMBER.ambermd.org https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua628U3io3o$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!wYPkBjofmsH6K2mZwPQr9-Ge6oEId6Rytj9n2aJul74SlJ1OLO0XiTVhQ8epgSCS1qSdugl-iBZAEFlgua628U3io3o$> _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Feb 15 2024 - 11:30:02 PST