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

From: Simon Kit Sang Chu <>
Date: Tue, 24 Jul 2018 10:44:28 +0800

Dear David,

Thanks for the info. I am also looked into the same tutorial. But I am
still confused to add soft-core potential atoms.

According to AMBER16 manual, it seems that I do not have to add dummy atoms
for my case.

> Note that a slightly different setup is required for using soft core
> potentials compared to older TI- implementations. Specifically, the
> difference is that to add or remove atoms without soft core potentials,
> they are transformed into interactionless dummy particles, so both end
> state prmtop files have the same number of atoms. When using soft core
> potentials instead, no dummy atoms are needed and the end states should be
> built without them.

So, I only have to set the timask and scmask on the atoms as in the
tutorial? All atoms present in timask while not in scmask will be
transformed without soft-core potential automatically?

Second, I already simulated methanol solvated without the topology of
ethanol. If I want to keep the coordinate and *velocity* for a new TI, how
should I prepare the files? The tutorial is preparing benzene and phenol
from a pdb file. Can I skip it by giving a rst file with coordinate and
velocity information?


David Cerutti <> 於 2018年7月24日週二 上午12:57寫道:

> 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 <
> wrote:
> > 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
> > _______________________________________________
> > AMBER mailing list
> >
> >
> >
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Received on Mon Jul 23 2018 - 20:00:03 PDT
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