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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 28 2019 - 06:00:06 PDT
