We assigned parameters in leap using “set default PBradii mbondi3’” and used igb = 8. The “blow up” begins with the initial step where the Antechamber-parameterized phenyl ring fragments, sending carbon and hydrogen tens of angstroms away within a few steps. The energies in the heating output appear reasonable, except for the bonding terms where the energies look much higher than expected. The gas phase simulations and the explicit solvent simulations are very stable on the microsecond timescale, so we are confident in everything, but the GB parameters. As far as the energies go, the minimization energy is roughly 49 kJ/mol higher than the energy at step 0 of the heating.
Thanks,
Taylor
________________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Thursday, March 3, 2016 9:51 PM
To: AMBER Mailing List
Subject: Re: [AMBER] GB Parameterization
Let us know which gb model you used, and how you assigned the intrinsic
radii in leap. You might also try without gb to to make sure that is the
problem. Does gas phase md work ok? Next, look closely at the md, using
ntpr=1. What do you mean by "blow up"?
On Mar 3, 2016 10:27 PM, "Taylor Harville" <taylor.harville.drake.edu>
wrote:
> We have been trying to run GB calculation on a system of multiwalled
> carbon nanotubes and a drug that we parameterized using antechamber. The
> minimization ran correctly for these systems, but the heating of each full
> system would always blow up at step one. We then tried just the
> parameterized drug with one carbon nanotube in the heating process. This
> ran for several steps where we were able to see the benzene ring on the
> drug explode. Our best guess is we are missing some GB parameters for this
> benzene ring that is causing this failure. How might we go about checking
> that our Antechamber-parameterized residue has reasonable GB parameters?
>
> Thanks,
> Taylor
>
>
>
> Taylor Harville
> Drake University Class of 2016
> Chemistry, Physics, and Mathematics
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Received on Fri Mar 04 2016 - 08:30:04 PST
