[gmx-users] Frozen covalent bound atoms

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jul 10 11:13:15 CEST 2013




On Jul 9, 2013 10:36 PM, "Nash, Anthony" <Anthony.Nash at warwick.ac.uk> wrote:

Hi all,

I would imagine this has been covered before, yet I don't think I have
unearthed the right search inquiry yet.

I want to make a dihedral angle along the length of a helical protein using
the vectors (A, B, C), (B, C, D), where B is a C-alpha on the helix
backbone, and A , C and D are fake atoms. I need the fake atom A to be
covalently bound/attached to C-alpha atom B, maintaining the constant angle
A-B-C. I then need to keep a totally frozen position of fake atoms C and D,
which are covalently bound in the order B-C-D.

All fake atoms must not interact with any atoms at all.

I don't want someone to tell me how to do it, I would just rather someone
told me a key word/link/section in the gromacs manual.

Many thanks
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