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)"
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
wrote:
> Dear all:
>
> I'm tryin
i mean i can not find pdb file for peptides.
On Mon, 02/01/2016 01:34 AM, Mark Abraham 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
Hi
I have a 1000ns simulation of gpcr protein. The protein structure have 7
helix.
1. How will I calculate the tilt of each helix?
2. If it has to be done by generating the index file, what groups are meant
to be added for index file?
3. What groups should be chosen when gmx bundle prompt to cho
