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--- Marcos S.A. On Fri, Apr 7, 2017 at 9:32 AM, Andreas Tosstorff < andreas.tosstorff.cup.uni-muenchen.de> wrote: > Thank you so much Marcos! > > > Can you please tell me how you obtained the BOND, ANGLE and DIHEDRAL > parameters and also the NONBON for CT and HC? > > > Best, > > Andy > > > On 04/07/2017 02:58 PM, Marcos Serrou do Amaral wrote: > > Hi Andy, > > > > I am sending to you ACN parameter files for this new 6-site model. > > In leap, you should use these lines: > > source leaprc.water.tip3p > > loadamberparams ACN_model.prm > > ACN = loadmol2 acn-model.mol2 > > > > Please, double check all parameters. > > > > HTH, > > > > > > --- > > Marcos S.A. > > > > > > On Wed, Apr 5, 2017 at 12:08 PM, Andreas Tosstorff < > > andreas.tosstorff.cup.uni-muenchen.de> wrote: > > > >> Dear all, > >> > >> > >> thank you for your replies! As David pointed out, setting up the > >> simulation was not the problem, but it's the separation of the two > >> solvents, as seen in the attached pictures. > >> > >> After the suggested google search I came across a paper titled "New > >> Six-site Acetonitrile Model for Simulations of Liquid Acetonitrile and > its > >> Aqueous Mixtures" by NIKITIN and LYUBARTSEV from 2007 (attached to this > >> mail). > >> > >> They report that they were able to succesfully simulate > water-acetonitrile > >> mixtures with their acetonitrile model. They furthermore state that > their > >> model can easily be included into AMBER. > >> > >> So how do I do this? > >> > >> Do I write an .frcmod and .lib file for acetonitrile using the > parameters > >> (Lennard-Jones parameters, charge, what else?) they published and then > >> rebuild my system in tleap? > >> > >> > >> This is completely new to me so I would really appreciate your help! > >> > >> > >> Best, > >> > >> Andy > >> > >> > >> > >> On 04/05/2017 05:00 PM, David Cerutti wrote: > >> > >>> You will not have an extra time with this if you want your simulation > to > >>> go > >>> a long time. For starters you can use the AddToBox utility in > amber/bin > >>> (run with no arguments to see the list of things you can do). That > will > >>> help you randomly mix acetonitrile and water initially (make sure to > >>> minimize before starting dynamics). > >>> > >>> But if you simulate just a few hundred acetonitriles and a thousand > waters > >>> (or whatever the ratio needs to be), then check after 50ns or so, and > find > >>> that they separate (which appears likely) you have as DAC said an > >>> imbalance > >>> in your FF and a parameter development problem. > >>> > >>> Once you get your solvents to stay mixed, round II: protein in solvent > >>> mixture. You could very well find that the protein gets coated in > >>> acetonitrile and that the acetonitrile gets leached out of solution in > the > >>> process. To determine whether THAT is realistic or not you will need > the > >>> right kind of experimental data. > >>> > >>> Dave > >>> > >>> On Apr 5, 2017 10:48 AM, "Sowmya Indrakumar" <soemya.kemi.dtu.dk> > wrote: > >>> > >>> Hi Andreas, > >>>> I am not sure if this is feasible. > >>>> Since you already know the ratio, you can do the following > >>>> 1.solvate you protein > >>>> 2.replace some of the water with the other molecule. For instance, > >>>> *addions* randomly replaces water with the ion you give. > >>>> Regards > >>>> Sowmya > >>>> ________________________________________ > >>>> From: David A Case [david.case.rutgers.edu] > >>>> Sent: Wednesday, April 05, 2017 4:37 PM > >>>> To: AMBER Mailing List > >>>> Subject: Re: [AMBER] Acetonitrile Water Mix > >>>> > >>>> On Wed, Apr 05, 2017, Andreas Tosstorff wrote: > >>>> > >>>>> I am trying to simulate a protein in a 60% acetonitrile, 40% water > >>>>> > >>>> mixture. > >>>> > >>>>> I observed that the two solvents arrange in layers rather than to > form a > >>>>> homogeneous mix. See the attached pictures and input files. > >>>>> Any advice on how to perform simulations with solvent mixtures? > >>>>> > >>>> Sounds like you already know how to perform the simulations. If these > >>>> two > >>>> liquids are supposed to be miscible, then there is likely an > inbalance in > >>>> your > >>>> force field. Try a Google search on something like "acetonitrile > water > >>>> force > >>>> field" to see what others have done in simulating this sort of > mixture. > >>>> > >>>> ....dac > >>>> > >>>> > >>>> _______________________________________________ > >>>> AMBER mailing list > >>>> AMBER.ambermd.org > >>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>> > >>>> _______________________________________________ > >>>> AMBER mailing list > >>>> AMBER.ambermd.org > >>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>> > >>>> _______________________________________________ > >>> AMBER mailing list > >>> AMBER.ambermd.org > >>> http://lists.ambermd.org/mailman/listinfo/amber > >>> > >> -- > >> M.Sc. Andreas Tosstorff > >> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie > >> Department Pharmazie > >> LMU München > >> Butenandtstr. 5-13 ( Haus B) > >> 81377 München > >> Germany > >> Tel.: +49 89 2180 77059 > >> > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > >> > >> > >> > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > > -- > M.Sc. Andreas Tosstorff > Lehrstuhl für Pharmazeutische Technologie und Biopharmazie > Department Pharmazie > LMU München > Butenandtstr. 5-13 ( Haus B) > 81377 München > Germany > Tel.: +49 89 2180 77059 > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Apr 07 2017 - 07:00:03 PDT