Re: [AMBER] MD with emap restraints, restraints have no effect

From: David A Case <>
Date: Sun, 4 Jul 2021 13:28:51 -0400

On Sat, Jul 03, 2021, Will Gerrard wrote:
>I am attempting to run a short MD simulation where the position of a serine
>residue and a ligand are constrained in order to force them into a
>conformation obtained from a different structure. The coordinates in the
>restraint are a small distance from the starting coordinates in the
>simulation, but the restraints seem to have absolutely no effect, even with
>very high force constant.

Can you be more explicit about exactly what the phrase "seems to have
absolutely no effect" means? Is there nothing related to EMAP in the output
file? You should see information that a map was being created, and there
should be an EMAP energy printed along with other components of the energy
every ntpr steps.

If the target map is a long way from the starting structure, the code may
have trouble figuring out which way to push things. Or, something else
might be awry. But first we need to know if you are getting EMAP results in
the output at all.

If you are seeing EMAP energies, try some experiments, e.g. where the target
structure is the same as the initial one, or just a little bit different,


AMBER mailing list
Received on Sun Jul 04 2021 - 10:30:02 PDT
Custom Search