[AMBER] How can we simulate only the ligand-bound domain of the protein?

From: Chetna Tyagi <cheta231.gmail.com>
Date: Fri, 28 Jun 2019 14:15:59 +0200

Dear Amber users,

I work with a big protein with roughly 1000 residues. The PDB structure has
missing residues which causes problem during equilibration.

Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 5803 11719 11720

This region is not useful for our study and I would like it to not be
involved. Sort of
like constraining it while only the ligand-bound domain undergoes
simulation.
Is there a way to do that which will also reduce the computational burden
and time?

If it is possible will there still be such errors? And should I just build
it and re-start?

Thanks--
Chetna
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Received on Fri Jun 28 2019 - 06:00:06 PDT
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