Hi Holly,
Waters were placed as if those dummy atoms had 1.5A radius. Given the
approach to water placement, this is unlikely to be a problem.
In case you missed it:
> > >> 1-4: angle 43748 43749 duplicates bond ('triangular' bond) or angle
> > >> ('square' bond)
> > In calculating the 1-4 nonbonded exclusion lists it was found that you
> > have either three atoms bonded into a triangle, or four atoms bonded
> > into a square. Are the atoms printed?
Bill
Hallel Freedman <hfreedma.ualberta.ca> wrote:
> Hi Bill,
> Thanks for your reply. The atoms that are referred to in the leap message
> are the cationic dummy atoms on the zinc. Do I need to worry about the
> bonding arrangement being referred to in the message, for these dummy
> atoms? These dummy atoms are also the ones for which no solvation radii are
> defined.
> Holly
>
>
>
> On Tue, Dec 3, 2013 at 11:26 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > On 12/3/2013 10:13 AM, Hallel Freedman wrote:
> > > Dear AMBER,
> > > I just wanted to make sure my message went through to the list yesterday.
> > > Thanks,
> > > Holly
> > >
> > >
> > > On Mon, Dec 2, 2013 at 5:46 PM, Hallel Freedman <hfreedma.ualberta.ca
> > >wrote:
> > >
> > >> Dear AMBER,
> > >>
> > >> I am setting up AMBER simulations of a proteins containing zinc fingers,
> > >> and I am trying to use the Zinc parameters from Yuan-Ping Pang, together
> > >> with the library and parameters downloaded from the website given on the
> > >> AMBER homepage:
> > >> When I try to save AMBER parm files I am getting messages like:
> > >>
> > >> 1-4: angle 43748 43749 duplicates bond ('triangular' bond) or angle
> > >> ('square' bond)
> > In calculating the 1-4 nonbonded exclusion lists it was found that you
> > have either three atoms bonded into a triangle, or four atoms bonded
> > into a square. Are the atoms printed?
> >
> > >>
> > >> Is this anything to worry about?
> > >>
> > >> One other thing bothered me a little bit - when I try to solvate the
> > >> system I get messages like:
> > >> (using default radius 1.500000 for D4)
> > >> (using default radius 1.500000 for D3)
> > >> (using default radius 1.500000 for D2)
> > >> (using default radius 1.500000 for D1)
> > >> I suppose this is not important, but I wanted to confirm this with you.
> > This suggests you have atoms with no radius parameter defined, which
> > might bite you later in saving prmtop.
> >
> > Bill
> >
> > >>
> > >> Thanks in advance,
> > >> Holly
> > >>
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> >
> >
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> >
> >
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Received on Thu Dec 05 2013 - 00:00:03 PST
