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-- Jason Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On May 16, 2012, at 8:10 PM, Олег Титов <titovoi.qsar.chem.msu.ru> wrote: > Hi, all. > > Is it possible to create two types of extra point charges in AMBER? > > I want to improve molecular electrostatics for a single molecule by > adding atomic dipoles and quadrupoles. It is important for me to use > GAFF in the same molecule where I put atomic multipoles, and, I guess, > there is no way to use atomic dipoles and quadrupoles (as in AMOEBA) > with GAFF (Correct me, please, if I'm wrong). To avoid this, I'm > trying to simulate dipole and quadrupole with 2 extra point charges (+ > atomic charge). The problem is that these two extra points are > different: one is "inside" R-X bond and the other is outside. I need > different atom types to set different valent angles (0.0 for "inner" > EP and 180 for "outer"). > > Amber manual states that extra points is "atoms with "EP" in their > names". So, I see no problem in using EP as names for all extra points > and creating 2 atom types (EP and LP or EP and ZP to avoid conflicts > with ff99SB's LP) for different positions. > > When I have only one EP in "outer" position, it is treated as EP and > everything works fine. > > Next, I want 2 different EPs. > I use frcmod ANGL section like this to have different EP positions: > ANGL > XX-br-LP 150.0 180.00 > XX-br-EP 150.0 0.00 > Both EP and LP atoms have "EP" as their atom names, but tleap seems to > recognize extra point only in EP and asks for angle parameters for > ca-br-LP and EP-br-LP. Ok, I add these parameters and get my prmtop > and prmcrd. Minimization in sander.MPI runs fine, but during it these > extra points are moved from their initial positions, so one is located > as "outer" extra point and the other's bond is perpendicular to R-X > bond (but bond angle should be 0.0 acccording to frcmod). Moreover, > during MD run both extra points are not kept in their ideal geometry . > "Outer" extra point seems to be fixed in space and bromine atom > oscillates somewhere nearby. "Inner" extra point spins around bromine > atom. May be interesting to note this fact: when I set ideal extra > point bond length to 0.1 Ang (to have "point" multipoles) sander > crashes with segfault somewhere in the end of the first MD iteration, > and when bond length is set to 0.5 Ang it seems to work fine, except > extra points are not treated as extra points. > > Can anybody tell me what I'm doing wrong? Is it possible to have two > types of extra points in sander? > > With Best Regards, > Oleg. > > > _______________________________________________ > 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 Sun May 20 2012 - 16:00:02 PDT