[gmx-users] gmx bundle
m.monsefi93 at ms.tabrizu.ac.ir
Mon Feb 1 07:42:18 CET 2016
i mean i can not find pdb file for peptides.
On Mon, 02/01/2016 01:34 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> That means the calculation failed somehow (e.g. you asked for a dihedral
> angle between four co-linear atoms, or divided by zero, or something like
> that) but we don't have any clues on why (at this stage).
> On Mon, Feb 1, 2016 at 6:22 AM Felix W.-H. Weng " target="_blank"><weiweng013 at gmail.com>
> > Dear all:
> > I'm trying to calculate kinks within alpha helices using gmx bundle. I
> > specify 4 Ca atoms from the helix top, bottom and kink separately in the
> > index file. And, I've used the option -na 1. But I keep getting the results
> > shown below.
> > @ title "Kink angles"
> > @ xaxis label "Time (ps)"
> > @ yaxis label "(degrees)"
> > @TYPE xy
> > 0 -nan
> > 500 -nan
> > 1000 -nan
> > 1500 -nan
> > 2000 -nan
> > 2500 -nan
> > 3000 -nan
> > 3500 -nan
> > 4000 -nan
> > 4500 -nan
> > 5000 -nan
> > ... ...
> > Does anyone know what "-nan" implies? Any advice would be appreciated,
> > thanks in advance.
> > Best,
> > Wei-Hsiang
> > --
> > Wei-Hsiang Weng (翁偉翔)
> > Department of Life Sciences
> > Tzu-Chi University
> > No.701, Sec. 3, Zhongyang Rd. Hualien 97004, Taiwan
> > Tel.: +886-975-232-245
> > --
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