Re: alchemical free energy simulations with parmtop

From: Hannes Loeffler (
Date: Mon Dec 01 2014 - 03:20:17 CST

Right. So namd explicitly disallows alchemical simulations when amber
is on. The error message is a bit weird though as it says that "AMBER
parameters" are not supported. A particular parameter set in itself can
hardly be the reason as it should be possible to introduce those trough
the PSF or Gromacs .top route (although the particular functional form
of the AMBER force fields may not be fully supported). I can't see
any safeguards against this in the code.

So, the question: why would the AMBER _force field_ not be supported?
Apparently there are a few differences in the functional forms of the
CHARMM and AMBER force fields which lack support for instance.


On Tue, 17 Jun 2014 10:35:59 +0100
Hannes Loeffler <> wrote:

> Hi,
> I am just looking through a few tutorials on how to do alchemical
> relative free energy calculations and see that they are all based on
> the PSF topology file format. I wonder if this is a requirement with
> namd or a AMBER parmtop file could be used instead.
> From what I understand there could be problems with the force fields
> terms in the parmtop because the way it works in namd is to create the
> morph pair as a single residue (and describe vanishing/appearing atoms
> in an associated PDB file). But is it possible with a parmtop
> provided the parmtop is created/manipulated accordingly? I guess
> this all boils down to how namd generates the force field terms
> internally for the two mutated molecules/fragments.
> Many thanks,
> Hannes.

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