AMBER Archive (2000)

Subject: Re: AMBER 6 and residual dipolar coupling

From: Vickie Tsui (vtsui_at_scripps.edu)
Date: Wed May 10 2000 - 12:04:11 CDT

Hi Fabio,

"iscale" is the number of additional variables to be optimized beyond the
3N structural parameters. In a residual dipolar coupling refinement, the
5 variables specifying the alignment tensor (s11, s22, s12, s13, s23) are
also optimized, thus iscale should be set to 5.

Thank you for catching the mistake on Section 1 of the sander manual,
which still says that only iscale=0 is supported. Sorry about the
confusion!

vickie

The Scripps Research Institute
10550 North Torrey Pines Road, TPC-15
La Jolla, CA 92037

TEL: (858)784-9788
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On Wed, 10 May 2000, Fabio Arnesano wrote:

> I am PhD student at the Magnetic Resonance Center of the University of
> Florence.
> I tried to use residual dipolar coupling as restraints in REM calculations
> with the new AMBER version.
> I prepared the input file using makeDIP_RST.
> The input is the following:
>
> &align
> ndip=60, dcut=-1.0, fj=0.1, dfac_al=60*-0.21341,
> s11=-2.336, s22=-2.081, s12=-1.087, s13=-0.343, s23=1.166,
> id(1)=47, jd(1)=48, dobs(1)= -0.14,
> id(2)=66, jd(2)=67, dobs(2)= -0.12,
> id(3)=88, jd(3)=89, dobs(3)= 0.15,
> id(4)=105, jd(4)=106, dobs(4)= 0.22,
> ...
> id(60)=1148, jd(60)=1149, dobs(60)= 0.36,
> &end
>
> When I run the minimization I get the following error and the program stops:
>
> iscale set incorrectly in align: 0 1
>
> Could you, please, tell me, what does it mean?
>
>
> Thanks in advance fou your help.
>
> Best regards
>
> Fabio Arnesano
>