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 Tue Dec 03 2013 - 11:00:02 PST
