AMBER Archive (2009)

Subject: RE: [AMBER] molecular mechanic minimisation with amber

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jan 14 2009 - 11:56:23 CST

> Hi
> I want to do a Molecular Mechanic Energy minimisation using amber:
>
> is it correct like this??
>
> sander -O -i sander.in -o sander.out -p prmtop -c inpcrd -r restrt
>
> with this sander.in
>
> initial minimisation prior to MD
> &cntrl
> imin = 1,
> maxcyc = 10000,
> ncyc = 5000,
> ntb = 0,
> igb = 0,
> ntc = 2,
> ntf = 2,
> cut = 12,
> /
>
> else? why i can do this?
> Thanks

Looks okay to me - the same caveats apply to what myself and Thomas replied
to this message on CCL last week. Sander's minimiser can only go so far - it
works with shake but not completely - i.e. it won't get you to a perfect
minimum etc etc. Try out some of the tutorials on
http://ambermd.org/tutorials/ for some examples of using AMBER.

All the best
Ross

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|\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 | PGP Key available on request |

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