[AMBER] Applying different restraints to different sets of atoms

From: Dmitry Suplatov <genesup.gmail.com>
Date: Mon, 25 Jul 2016 15:38:52 +0300

Dear colleagues,

I want to simulate movement of one particular part of my protein (i.e.
part1) while the rest of the protein (i.e., part2) should be left intact.
For this I plan to apply positional restraints to the whole molecule and
then during the relaxation period I want to gradually remove restraints
from the part1 while retaining the restraints on the part2.

I know how to apply restraints using restraintmask:

ntr=1, ! Restrain atoms using a harmonic potential
restraintmask='!(:WAT,Na+,Cl-) & !.H=', ! Apply restraints to all
non-hydrogen atoms of all residues except water and ions
restraint_wt=3, ! Force constant (kcal/(mol Angstroms^2))

But this will apply restraints to only one set of atoms, while my aim is to
have two set of atoms with two different restraints applied.

Can I do this in Amber14?

Thank you for your time.
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Received on Mon Jul 25 2016 - 06:00:03 PDT
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