Hi Simon,
That's my understanding--maybe others have better ways.
If you have both methanol and ethanol equilibrated, you only can use one, right?
You need to match the common atoms--does that make sense? If your common atoms do not have the same coordinates, how can Amber handle them as common atoms?
For SC atoms, they don't need to be matched. So you don't need to match H in methanol to CH3 in ethanol.
For example, if you have only ethanol equilibrated, I would create a pdb for ethanol, make a copy of it, and in the copied pdb, change the residue name into methanol, delete H's in CH3, and change C into H--now the copy is a "methanol" pdb.
Use tleap to merge this original ethanol with the modified "methanol" pdb. Create the combined topology and crd files.
Then in tiMerge define -CH2-OH as common atoms, and CH3- (ethanol) and H- (methanol) as SC atoms.
Taisung
-----Original Message-----
From: Simon Kit Sang Chu <simoncks1994.gmail.com>
Sent: Wednesday, July 25, 2018 4:22 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Soft-core alchemical transformation in TI
Sorry, one more thing to add. So even if I am using soft-core potential, I still have to match their coordinates? Specifically to my case, how should I map the atoms H in methanol to CH3 in ethanol? I am a bit confused.
Thanks,
Simon
Simon Kit Sang Chu <simoncks1994.gmail.com> 於 2018年7月26日週四 上午12:17寫道：
> Hi Taisung,
>
> So there seems to be no way to bypass pdb and manually merge them with
> the TER card even with inpcrd. If I am modifying the coordinates, I
> may not be able to restore all equilibrated atom coordinates.
>
> Please correct me if I am wrong.
>
> Regards,
> Simon
>
> <accuratefreeenergy.gmail.com> 於 2018年7月26日週四 上午12:11寫道：
>
>> Hi Simon,
>>
>> Here is what I usually do--other developers may have other
>> better
>> ways:
>>
>> 1. Create PDB files for your methanol and ethanol. You can use
>> cpptraj to convert your coordinate/restart files into pdb files. Or
>> if you only have ethanol--create one for it, make a copy, and change
>> the residue names in the copied one so that it becomes a "methanol" pdb.
>> 2. Merge your two PDB files into one by hand--at this stage, you also
>> may modify the coordinates for each atom so that, for example, the
>> common atoms have exactly the same coordinates.
>> 3. Use tleap to read the combined PDB and produce the combined
>> topology/crd files.
>> 4. Use tiMerge to merge the common parts.
>>
>> Taisung
>>
>> -----Original Message-----
>> From: Simon Kit Sang Chu <simoncks1994.gmail.com>
>> Sent: Wednesday, July 25, 2018 4:59 AM
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
>>
>> 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
>> > > > _______________________________________________
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Received on Wed Jul 25 2018 - 10:00:02 PDT
