Hi
-s 2 in antechamber just defines level of verbosity and has nothing to do
with gaff or gaff2. The atom types are defined by the -at flag where you
must choose gaff2 because the default for -at is gaff.
However, I landed in the same situation as yours with the following
combination of force fields for my system
ff19SB + DNA.OL15 + gaff2 + FB3 waters.
When I changed this combination to
ff14SB + DNA.OL15 + gaff2 + TIP3P waters, the simulations do not crash.
On Saturday, October 17, 2020, Liao <liaojunzhuo.aliyun.com> wrote:
> Thanks for the answer Dr Case,
>
> I just now realized a subtlety regarding gaff and gaff2 in my
> preparations.
> In tleap, I sourced leaprc.gaff2, but in parmchk2 for generating the
> frcmod file, I never specified the -s 2 option for gaff2. It ran by default
> which is gaff. My input mol2 atom types are also gaff, not gaff2 as saved
> by Chinera. Never knew of the -s 2 option until you brought up differences
> between gaff and gaff2.
>
> I wonder whether the whole time I was using gaff or gaff2, with the above
> mentioned procedure? Was sourcing leaprc.gaff2 compatible with gaff atom
> types, since it never reported an error?
>
> Thank you.
>
> > On Oct 15, 2020, at 1:32 PM, David A Case <david.case.rutgers.edu>
> wrote:
> >
> > On Thu, Oct 15, 2020, Liao wrote:
> >
> >> Thanks there, I could try preparing that, though for using vlimit=10,
> >> does this seem like an appropriate solution? What’s the unit of this
> >> parameter, the manual doesn’t say it. The trajectory as viewed and post
> >> MD-MMGbsa energy from it looks normal to me.
> >
> > Units of vlimit are internal velocity usits: Å/(20 fs). vlimit=10 is
> > OK, especially if it only get's triggered occasionally. But it does
> > look like something in your ligand allows large forces: do you have any
> > hydrogens with zero vdW radii? (This could happen on a ligand if you
> > were, for example, using gaff rather than gaff2.) Hydrogens are a
> > common source of headaches for non-standard residues.
> >
> > ....dac
> >
> >
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--
Best Regards
Elvis
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Received on Fri Oct 16 2020 - 19:30:02 PDT
