AMBER Archive (2007)

Subject: Re: AMBER: Offending restraints????

From: saccenti_at_cerm.unifi.it
Date: Tue Jun 26 2007 - 10:34:37 CDT

GOSH!

These values come for experimental NMR restrains that have been randomly
perturbed.

That means that I need to increase all the R values below 1.8?

Thanks
edo

> On Tue, Jun 26, 2007, saccenti_at_cerm.unifi.it wrote:
>
>> I noitice that, but that values are created by the program...
>
>> >> ERROR: r1 -> r4 (and r1a -> r4a) must be monotonically
>> >> increasing; Offending restraint:
>> >> ******
>> >> HB ( 812)-COM ( -1) NSTEP1=
>> >> 0 NSTEP2=
>> >> 0
>> >> R1 = 1.300 R2 = 1.800 R3 = 1.610 R4 = 2.110 RK2 =
>
> By default, the makeDIST_RST program assumes a lower bound of 1.8
> angstroms.
> This makes sense for ordinary "NMR" restraints between atoms that are not
> bonded to each other.
>
> If you have upper bounds (as above) of 1.61 Angstroms (!), you will have
> to
> either create the restraints by hand, or manually modify the DISANG file
> for
> these unusual restraints.
>
> ...good luck...dac
>
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-- 
Dr Edoardo Saccenti
CERM Magnetic Resonance Center
University of Florence
Fiorgen Foundation
Via Luigi Sacconi n° 6
50019 Sesto Fiorentino
(FI) Italy
Tel: +39 055 4574281

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