Re: [AMBER] Soft-core alchemical transformation in TI

From: David Cerutti <>
Date: Mon, 23 Jul 2018 12:57:24 -0400

There are two ways to do it:

1.) Map the extra dummy atoms of ethanol to methanol: in this way, each
atom has its exact mapped partner in methanol and ethanol, and they will
have exactly the same coordinates. The masses of atoms do not affect the
binding free energy so you don’t need to worry.

2.) Treat different atoms as “softcore regions.” In this way, the
different atoms will move independently.

The second way is preferred, as the result will usually be much more stable.

You can find the parameter settings in the manual (p426) and a step-by-step
example in

Best of luck!

Dave and Taisung

On Mon, Jul 23, 2018 at 11:12 AM Simon Kit Sang Chu <>

> Hi everyone,
> I am planning to transform a methanol into an ethanol. I did a simulation
> of pure methanol solvated in water. I want to keep all the coordinates and
> velocities, including common hydrogens, in the restart in amber format. I
> have two concerns right now.
> First, to transform from methanol to ethanol, I have to cut a hydrogen out
> from methanol and append a CH3- from the broken end. I briefly look into
> AMBER manual and dummy atoms are necessary for pmemd preparation. Atoms
> transformed must also have the same masses so I cannot transform the
> hydrogen truncated into the new carbon. In that case, how should the
> coordinate files be written? Can I skip creating a pdb with a crd and
> include the hydrogens?
> Second, I am new to AMBER and I am not sure if it is using dual topology.
> If so, the CH3- will still be bonded with methanol while having no LJ and
> electrostatics. However, will the thermal motion created by the thermostat
> alter the motion of methanol even at lambda = 0? If I am transforming a
> methanol to a hexanol, the methanol motion would largely be random due to
> the higher momentum of the "invisible" (CH2)4-CH3 tail.
> I appreciate any advice. Sorry for the long mail!
> Regards,
> Simon
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Received on Mon Jul 23 2018 - 10:00:02 PDT
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