Thanks a lot for explaining, Bill.
Holly
On Thu, Dec 5, 2013 at 12:46 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> 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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Received on Thu Dec 05 2013 - 07:00:02 PST
