Hello all,
I am using ff99SB to model an antibody with carbohydrate ligands.
When I use something like [ restraintmask=':1-500' ], all atoms within this
500 residues will be restrained, right?
But I also heard someone only restraining the heavy atoms, or only
restraining the backbone atoms.
I wonder if this really matters for my system. As far as I know,
equilibration is aimed at getting the temperature and pressure right, mainly
for the solvent. And as long as we are going to do a 'real' MD production
run without restraints, it should not matter too much how we restrained the
antibody and ligands.
I am not if I am right about this. Any suggestions?
Thanks,
Yun
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Oct 29 2011 - 17:30:02 PDT
