AMBER Archive (2009)

Subject: RE: [AMBER] semiempirical copper

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Dec 03 2009 - 11:28:45 CST

Hi Jacopo,

> i would like to run a QM/MM simulation of a metalloprotein with a
> copper
> atom.
>
> Are there semiempirical methods to do it in Amber? To date i'was not
> able
> to find it in the manual.
>
> Could anybody give me any advices about this type of simulations.

Copper is not currently available due to the need for d-orbitals which are
not yet supported (but should be in a future release). Hence right now you
cannot include copper in your QM region unless you use something like Pupil
and hook it to an external program but this of course comes with a massive
performance hit and the inability to run with full periodic boundaries and
long range electrostatics.

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |

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