Re: (No Subject)

From: Jarrod Smith <>
Date: Thu 08 Mar 2001 09:45:51 -0600

monica jain wrote:
> Hello,
> I have made a 7 column input file using NMR distance restraint but it is not accepting interproton distances less than 1.8.On running minimization it says check min.out & in that it gave following error -
> r1 -> r4 (and r1a -> r4a) must be monotonically increasing; Offending restraint:
> ******
> H2'1( 26)-H2'2( 27) NSTEP1= 0 NSTEP2= 0
> R1 = 1.300 R2 = 1.800 R3 = 1.370 R4 = 1.870 RK2 = 20.000 RK3 = 20.000
> I would be obliged for any help.
> Thank you in advance.
> Monica

This is because makeDIST_RST was written assuming the input would be
proton-proton distances, and 1.8 Angstrom is the sum of their Van der
Waals radii. So they won't be getting closer than that in any case.

If you really have a system which needs the lower bound set smaller than
that (I can't think of how you would have this unless there was a bond
defined between your two atoms and it had a force constant of zero),
then you will need to edit line 1132 of
$AMBERHOME/src/nmr_aux/prepare_input/makeDIST_RST.c and plug in your new

Jarrod A. Smith
Research Asst. Professor, Biochemistry
Asst. Director, Center for Structural Biology
Computation and Molecular Graphics
Vanderbilt University
Received on Thu Mar 08 2001 - 07:45:51 PST
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