AMBER Archive (2004)

Subject: Re: AMBER: xleap console message

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 19 2004 - 11:40:46 CDT

On Mon, Apr 19, 2004, Guanglei Cui wrote:
>
> While I was building a molecule with all home-cooked parameters, I saw
> the following messages from Xleap console
>
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-N2-Zn1-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-S1-Zn1-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-O2-Zn1-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
>
> Is this something I should worry about? The unit is checked OK.

You are probably OK, but should really do two things: (1) use addAtomTypes
to tell LEaP about the zinc atom; (2) hand-check that the torsions involving
the zinc have the values you want them to have.

...good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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