AMBER Archive (2004)

Subject: Re: AMBER: Question on tleap of amber8

From: David A. Case (case_at_scripps.edu)
Date: Mon Dec 20 2004 - 11:27:07 CST

On Mon, Dec 20, 2004, Okimoto Noriaki wrote:
>
> When I made topology file using tleap, tleap told the following message.

> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-N1-C7-*
> +--- With Sp0 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
>
> After that, I add the atom types, elements, hybridizations of ligand
> molecule into leaprc file,
> Besides, I found that the result of md calculation was changed by the
> addition in leaprc.

What was it that changed? Did you look at the energy for a single
configuration, both before and after? You can use "readparm" to examine
the torsional contributions for the two prmtop files, and see if/how they
differ.

...dac

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