Re: [AMBER] Multidihedral and histogram analysis

From: Daniel Roe <>
Date: Fri, 1 Nov 2013 10:20:37 -0600


On Fri, Nov 1, 2013 at 9:48 AM, Fabrício Bracht <> wrote:
> Hi. I have two questions. By using the muldihedral chip command, the
> resulting values are only the chi1 dihedral values or something else.

I'm not 100% sure what you mean here. The 'chip' keyword means
'protein chi', and 'chin' is 'nucleic chi' if that helps clear things

> Second, the command hist:
> multidihedral chi1 chip resrange 15,16,204,206,259,264 out chi.dat
> runanalysis hist chi1[*100] out hist-dihed.gnu
> fails with the following warning:
> [runanalysis hist chi1 [*100] out hist-dihed.gnu]
> Dataset chi1 not found.

This is actually the same issue you were having with the 'hbond'
command. When the 'multidihedral' action is initialized it knows what
dihedrals you want to look for, but does not know what dihedrals it
will actually find in any of the topologies you might process, so
until you've actually processed frames the dihedral data sets are not
created. The solution is to put a "run" statement between
'multidihedral' and 'runanalysis'.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Nov 01 2013 - 09:30:03 PDT
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