Dear Taisung and Dave,
I read the tiMerge command and its usage in page 429 of the manual. I
notice it is feeding a single topology file ti.prmtop instead of two.
To run parmed:
>
> parmed -p ti.prmtop -i merge.in
>
>
>
> The input for parmed (merge.in) looks like this:
>
> loadRestrt ti.inpcrd set
>
> Overwrite True
>
> tiMerge :1-5 :6-10 :3 :8
>
> outparm ti_merged.prmtop ti_merged.inpcrd
>
> quit
>
>
In my case of methanol and ethanol, I do not have a merged topology file
yet. How should I merge the restart files and individual topologies?
Thanks!
Simon
<accuratefreeenergy.gmail.com> 於 2018年7月24日週二 下午8:50寫道：
> Hi Simon,
>
> Here are our answers:
>
> >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?
>
> Yes. All atoms in timask but not in scmask will be treated as
> common atoms, provided that each common atom can find its partner atom and
> all common atom pairs have the same coordinates (up to 0.1 A tolerance).
>
> >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?
>
> You could do that but not just directly using a methanol restart
> file. The restart file only contains methanol coordinates. You need a
> restart files containing both methanol and ethanol coordinates--although
> they could be the same. You might use the tiMerge utility (manual page
> 275) in the ParmED module (manual page 252) to merge a methanol restart
> file w/ an ethanol restart file. It takes some time to learn how to use it
> but it will be very useful if you want to TI/FEP/MBAR calculations often.
>
> Taisung & Dave
>
>
> -----Original Message-----
> From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> Sent: Monday, July 23, 2018 10:44 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
>
> 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.
>
>
>
> Thanks,
> Simon
>
> David Cerutti <dscerutti.gmail.com> 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
> http://ambermd.org/tutorials/advanced/tutorial9/index.html.
> >
> > Best of luck!
> >
> > Dave and Taisung
> >
> >
> > On Mon, Jul 23, 2018 at 11:12 AM Simon Kit Sang Chu <
> > simoncks1994.gmail.com>
> > 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
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Jul 25 2018 - 02:00:02 PDT
