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
>> > > > _______________________________________________
>> > > > 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
>> > >
>> > _______________________________________________
>> > 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
>> >
>> _______________________________________________
>> 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
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 25 2018 - 09:30:04 PDT
