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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical Physics, Biomedical Engineering, and Chemical Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Wed, Jul 12, 2017 at 10:04 AM, David Case <david.case.rutgers.edu> wrote: > On Wed, Jul 12, 2017, Dan Roe wrote: >> >> I think you are missing this in your script: >> WAT=TP4 > > No: "T4E" (not "TP4") is the abbrevation needed here. > > A side note: helping people get this right is an important benefit > of using top-level leaprc files (in this case, leaprc.water.tip4pew), rather > than trying to load all the underlying files yourself. Using a leaprc.water.* > file will also help ensure that you get the correct ion parameters that go > along with the water model you have chosen. > > A further note: Using "set deault flexiblewater on" should (generally) only > be done for water models designed to be flexible, such as spcfw. The "tip" > models (including tip4pew) were parameterized to be rigid; the thermodynamic > properties of a "flexible" tip4pew water are probably far from experiment. > > [Expanded version: I use the word "generally" above because of course there > are exceptions, and the original poster is likely to be familiar with these > issues. I mainly want to dissuade users from thinking something like this: > "well, *real* water is flexible, so it must be good to turn flexible water > on." The vast majority of Amber simulations should use rigid waters.] > > ....dac > > > _______________________________________________ > AMBER-Developers mailing list > AMBER-Developers.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber-developers _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Wed Jul 12 2017 - 11:00:02 PDT