[gmx-users] gmx bundle

[m.monsefi93]

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:
> Hi,
> 
> 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).
> 
> Mark
> 
> On Mon, Feb 1, 2016 at 6:22 AM Felix W.-H. Weng " target="_blank"><weiweng013 at gmail.com>
> wrote:
> 
> > 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.