AMBER Archive (2009)

Subject: Re: [AMBER] RDC and alignment tensor

From: case (
Date: Tue Oct 20 2009 - 07:24:45 CDT

On Mon, Oct 19, 2009, Eliana Asciutto wrote:
> This is the new input file:

> RST.dip file:
> &align
> ndip=47, gigj = 47*-3.163, dwt=47*0.05,
> freezemol=.true.,num_datasets=1,
> dataset=1
> id(1)=76, jd(1)=77, dobsl(1)=0.2, dobsu(1)=20.2,
> id(2)=111, jd(2)=2, dobsl(2)=-7.5, dobsu(2)=12.5,
> id(3)=199, jd(3)=200, dobsl(3)=-18.9, dobsu(3)=1.1,
> id(4)=244, jd(4)=245, dobsl(4)= -23.4, dobsu(4)=3.4,
> id(5)=437, jd(5)=438, dobsl(5)=3.5, dobsu(5)=23.5,
> id(6)=470, jd(6)=471, dobsl(6)=-35.2, dobsu(6)=-15.2,
> id(7)=481, jd(7)=482, dobsl(7)=3.4, dobsu(7)=23.4,
> id(8)=642, jd(8)=643, dobsl(8)=7.3, dobsu(8)=27.3,
> id(9)=657, jd(9)=658, dobsl(9)=-9.5, dobsu(9)=10.5,
> id(10)=668, jd(10)=669, dobsl(10)=3.4, dobsu(10)=23.4,
> id(11)=724, jd(11)=725, dobsl(11)=-12.6, dobsu(11)=7.4,
> id(12)=853, jd(12)=854, dobsl(12)=4.2, dobsu(12)=24.2,
> id(13)=860, jd(13)=861, dobsl(13)=4.6, dobsu(13)=24.6,
> id(14)=920, jd(14)=921, dobsl(14)=-12.6, dobsu(14)=7.4,
> id(15)=944, jd(15)=945, dobsl(15)=2.0, dobsu(15)=22.0,

Looks like you are in for some debugging here. A few comments/questions:

You values for dobsl and dobsu are very far apart from each other; is this
what you really want? It looks like you won't really have any effective
restraints at all with such input data.

Set dcut to a negative value (e.g. -1.0) so that all the output data will be
printed. Try maxcyc=1. Try an arbitrary set of non-zero values for s11, etc.

Before, you got additional output (listing of the alignment tensor as all
zeroes, etc.) Try to figure out why you didn't get that additional output
this time.

The examples in amber10/test/rdc show several examples of running alignment
jobs -- even the Run.csa and Run.csa_min use dipolar couplings. Make sure the
test cases work, and try to figure out why your inputs are different from
the ones in the test cases.

...good luck...dac

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