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 - 09:30:04 PDT
