Hi Taisung,
Sorry for the delay. I tried to learn it by mutating a protein instead in
the past few days, from ACE-ALA*-NME* to ACE-ALA*-ALA-NME*. However, error
always persists. I hope I am not misunderstanding the command.
*The merged PDB:*
ATOM 1 H1 ACE 1 2.000 1.000 -0.000 1.00 0.00
H
ATOM 2 CH3 ACE 1 2.000 2.090 0.000 1.00 0.00
C
ATOM 3 H2 ACE 1 1.486 2.454 0.890 1.00 0.00
H
ATOM 4 H3 ACE 1 1.486 2.454 -0.890 1.00 0.00
H
ATOM 5 C ACE 1 3.427 2.641 -0.000 1.00 0.00
C
ATOM 6 O ACE 1 4.391 1.877 -0.000 1.00 0.00
O
ATOM 7 N ALA 2 3.555 3.970 -0.000 1.00 0.00
N
ATOM 8 H ALA 2 2.733 4.556 -0.000 1.00 0.00
H
ATOM 9 CA ALA 2 4.853 4.614 -0.000 1.00 0.00
C
ATOM 10 HA ALA 2 5.408 4.316 0.890 1.00 0.00
H
ATOM 11 CB ALA 2 5.661 4.221 -1.232 1.00 0.00
C
ATOM 12 HB1 ALA 2 5.123 4.521 -2.131 1.00 0.00
H
ATOM 13 HB2 ALA 2 6.630 4.719 -1.206 1.00 0.00
H
ATOM 14 HB3 ALA 2 5.809 3.141 -1.241 1.00 0.00
H
ATOM 15 C ALA 2 4.713 6.129 0.000 1.00 0.00
C
ATOM 16 O ALA 2 3.601 6.653 0.000 1.00 0.00
O
ATOM 17 N NME 3 5.846 6.835 0.000 1.00 0.00
N
ATOM 18 H NME 3 6.737 6.359 -0.000 1.00 0.00
H
ATOM 19 CH3 NME 3 5.846 8.284 0.000 1.00 0.00
C
ATOM 20 HH31 NME 3 4.819 8.648 0.000 1.00 0.00
H
ATOM 21 HH32 NME 3 6.360 8.648 0.890 1.00 0.00
H
ATOM 22 HH33 NME 3 6.360 8.648 -0.890 1.00 0.00
H
END
ATOM 1 H1 ACE 4 2.000 1.000 -0.000 1.00 0.00
H
ATOM 2 CH3 ACE 4 2.000 2.090 0.000 1.00 0.00
C
ATOM 3 H2 ACE 4 1.486 2.454 0.890 1.00 0.00
H
ATOM 4 H3 ACE 4 1.486 2.454 -0.890 1.00 0.00
H
ATOM 5 C ACE 4 3.427 2.641 -0.000 1.00 0.00
C
ATOM 6 O ACE 4 4.391 1.877 -0.000 1.00 0.00
O
ATOM 7 N ALA 5 3.555 3.970 -0.000 1.00 0.00
N
ATOM 8 H ALA 5 2.733 4.556 -0.000 1.00 0.00
H
ATOM 9 CA ALA 5 4.853 4.614 -0.000 1.00 0.00
C
ATOM 10 HA ALA 5 5.408 4.316 0.890 1.00 0.00
H
ATOM 11 CB ALA 5 5.661 4.221 -1.232 1.00 0.00
C
ATOM 12 HB1 ALA 5 5.123 4.521 -2.131 1.00 0.00
H
ATOM 13 HB2 ALA 5 6.630 4.719 -1.206 1.00 0.00
H
ATOM 14 HB3 ALA 5 5.809 3.141 -1.241 1.00 0.00
H
ATOM 15 C ALA 5 4.713 6.129 0.000 1.00 0.00
C
ATOM 16 O ALA 5 3.601 6.653 0.000 1.00 0.00
O
ATOM 17 N ALA 6 5.846 6.835 0.000 1.00 0.00
N
ATOM 18 H ALA 6 6.737 6.359 -0.000 1.00 0.00
H
ATOM 19 CA ALA 6 5.846 8.284 0.000 1.00 0.00
C
ATOM 20 HA ALA 6 5.332 8.648 -0.890 1.00 0.00
H
ATOM 21 CB ALA 6 5.135 8.833 1.232 1.00 0.00
C
ATOM 22 HB1 ALA 6 5.643 8.485 2.131 1.00 0.00
H
ATOM 23 HB2 ALA 6 5.150 9.922 1.206 1.00 0.00
H
ATOM 24 HB3 ALA 6 4.102 8.485 1.241 1.00 0.00
H
ATOM 25 C ALA 6 7.266 8.832 0.000 1.00 0.00
C
ATOM 26 O ALA 6 8.229 8.068 -0.000 1.00 0.00
O
ATOM 27 N NME 7 7.394 10.161 0.000 1.00 0.00
N
ATOM 28 H NME 7 6.572 10.747 0.000 1.00 0.00
H
ATOM 29 CH3 NME 7 8.692 10.805 -0.000 1.00 0.00
C
ATOM 30 HH31 NME 7 9.475 10.046 -0.000 1.00 0.00
H
ATOM 31 HH32 NME 7 8.789 11.427 -0.890 1.00 0.00
H
ATOM 32 HH33 NME 7 8.789 11.427 0.890 1.00 0.00
H
END
*tleap:*
source leaprc.protein.ff14SB
all = loadpdb A-cat.pdb
saveamberparm all all.prmtop all.rst
quit
*parmed:*
parmed all.prmtop
loadrestrt all.rst
timerge :1-3 :4-7 :3 :6-7
TiMergeError: The number of nonsoftcore atoms in mol1mask and mol2mask must
be the same.
This is a very basic question, but I thought the number and coordinates of
residue 1-2 and 4-5 are the same. Why would I still get the error?
Regards,
Simon
<accuratefreeenergy.gmail.com> 於 2018年7月26日週四 上午12:37寫道：
> 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
> >> > > > _______________________________________________
> >> > > > AMBER mailing list
> >> > > > AMBER.ambermd.org
> >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > >
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> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> >
> >> > _______________________________________________
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> >> >
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Received on Sat Jul 28 2018 - 08:30:02 PDT
