[gmx-users] tilt angle

Shreyas Kaptan shreyaskaptan at gmail.com
Wed Jun 20 11:47:05 CEST 2018

If you fire the 'gmx make_ndx' you will find that there is a section there
for c-alpha atoms. By combining the c-alpha group with the index of the
protein with the "&" operator (without quotations) should work.

On Wed, Jun 20, 2018 at 8:41 AM Fa Hamedi <hamedifatemeh1367 at gmail.com>

> Hi,
> I am new in this mailing list and I have a question:
> I haveve performed MD simulation of transmembrane protein using
> Gromacs. Now, I want to calculate the angle of tilt of the
> transmembrane protein against the bilayer normal. I know that I can
> use
> gmx helixorient but I don t know how should make index file?? My
> protein is a dimer helix and has 61 residues. I don t know how choose
> carbo alpha atoms for calculating tilt angle! can anyone help me??
> Thank you.
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Shreyas Sanjay Kaptan

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