Re: [AMBER] Converting Amoeba .xyz for use with Amber

From: case <case.biomaps.rutgers.edu>
Date: Sat, 14 Dec 2013 11:09:50 -0500

On Fri, Dec 13, 2013, Eugene Yedvabny wrote:
>
> I am still stuck with Amber -> Tinker -> Amber conversion necessary to get
> Amoeba prmtop and inpcrd. It appears that my first assumption about NHE ->
> NH2 conversion being the culprit is wrong. The error is actually caused by
> the disulfide bridge: Tinker recognizes CYX residues and automatically
> makes a bond between them (yay!) but then analyze.x chokes on the
> multipoles for that bridge (nay!):
>
> Atomic Multipole Parameters :
>
> Atom Coordinate Frame Definition Multipole Moments
> 2 2 0 0 0.00000
> 0.00000 0.00000 0.00000
> 0.00000
> 0.00000 0.00000
> 0.00000 0.00000 0.00000
>
> I am attaching the whole analout file, but the above is an example of a
> section that confused tinker_to_amber.

Thanks for finding this! It looks like somehow it should be easy to fix.

I'm cc-ing this to Jay Ponder to see if this is what is expected for S-S
bonds.

Try this: remove the lines like those above, and re-run tinker_to_amber. Do
you get the same energies then in tinker and in pmemd.amoeba or sander?

It's easy enough to change tinker_to_amber to handle this, if that is what
needs to be done.

...regards...dac



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Received on Sat Dec 14 2013 - 08:30:02 PST
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