AMBER Archive (2009)

Subject: Re: [AMBER] AMBER: chiral restraint on protein

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Feb 11 2009 - 06:56:05 CST

On Tue, Feb 10, 2009, amit jain wrote:

> After going through tutorial Replica Exchange Simulations with AMBER 10
> TUTORIAL A7,
> using makeCHIR_RST gives
> <http://ambermd.org/tutorials/advanced/tutorial7/files/ala10_chir.dat>
> ala10_chir.dat <http://ambermd.org/tutorials/advanced/tutorial7/files/ala10_chir.dat>
>
> #
> # chirality for residue 2 atoms: N C HA CB
> &rst iat=7,15,10,11,
> r1=10., r2=60., r3=80., r4=130., rk2 = 10., rk3=10., &end
> #
> # chirality for residue 3 atoms: N C HA CB
> &rst iat=17,25,20,21, &end
> #
>
> Only residue 2 is given r1,r2,r3,r4, rk2, rk3, None of the other residues
> were given r values.
> Do I have to put in these values by manually going in chir.dat file, Or
> there are some default value which it takes for other residues.

These values are "sticky": the default is the most recent value seen.
So, r1, etc only needs to be given once if the values are not changing.

[I would have sworn that this was in the Users' Manual, but I don't see
it now, so we'll have to update that.]

...regards...dac

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