Hi everyone,
I am doing MD simulation of protein-ligand complex. I was needed to apply
restraint_wt on protein backbone and ligand heavy atoms only during
minimization (50 kcal/mol −Å) and heating (5 kcal/mol −Å) but by mistake I
applied it to all the atoms of ligand and some of the TIP3P water molecules
along with protein backbone. I have done NPT equilibration for 2.4 ns
before production run.
I have a question, will it affect the MD calculations from the scenario
when I don't have to apply restraint on ligand's hydrogen atoms and some of
the TIP3P water molecules?
Thanks
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 30 2017 - 05:30:03 PDT
