Hi,
Thanks for the reply. The index 44 has indeed zero force constant.
We are moving forward and using the oldff/leaprc.ff14SB.
Best,
João
On Wed, Feb 1, 2017 at 2:27 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> The real test is "are the forces and energies you get different". If I
> recall correctly, in this case the differences you refer to are from the
> addition of "placeholder" end dihedrals (i.e. Dihedrals with 0.0 force
> constant) which were previously missing. I think the reason was to prevent
> so-called "wild card" dihedrals from being improperly applied (others
> please correct me if I'm wrong here). The bottom line is that the energies
> obtained with the old topology and new should be identical for the same
> coordinates. Please let us know if this is not the case.
>
> -Dan
>
> On Tue, Jan 31, 2017 at 3:34 PM Joao Damas <j.damas.acellera.com> wrote:
>
> > Hi guys,
> >
> > We wanted to change from AmberTools15 to AmberTools16, and we saw in the
> > changelog (http://ambermd.org/changelog.html) about the new
> specifications
> > for choosing force-fields.
> >
> > For now, we were at least testing if oldff/leaprc.ff14SB in AmberTools16
> > gave the same results as the leaprc.ff14SB in AmberTools15.
> >
> > As a matter of fact, it does not. The initial difference that caught my
> > attention was:
> >
> > 591c596
> > < AMBER General Force Field for organic molecules (Version 1.7, Nov 2013)
> > ---
> > > AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
> >
> > So I changed to use the gaff.dat from AmberTools15.
> >
> > After that change, the entire diff between leap.log files using
> > AmberTools15 and AmberTools16 is:
> >
> > 1c1
> > < log started: Tue Jan 31 20:21:26 2017
> > ---
> > > log started: Tue Jan 31 21:15:45 2017
> > 48c48
> > < Loading parameters:
> > /home/joao/maindisk/software/amber14/dat/leap/parm/lipid14.dat
> > ---
> > > Loading parameters:
> > /home/joao/maindisk/software/amber16/dat/leap/parm/lipid14.dat
> > 55c55
> > < Loading library:
> > /home/joao/maindisk/software/amber14/dat/leap/lib/lipid14.lib
> > ---
> > > Loading library:
> > /home/joao/maindisk/software/amber16/dat/leap/lib/lipid14.lib
> > 65,67c65,67
> > < > source leaprc.ff14SB
> > < ----- Source:
> > /home/joao/maindisk/software/amber14/dat/leap/cmd/leaprc.ff14SB
> > < ----- Source of
> > /home/joao/maindisk/software/amber14/dat/leap/cmd/leaprc.ff14SB done
> > ---
> > > > source oldff/leaprc.ff14SB
> > > ----- Source:
> > /home/joao/maindisk/software/amber16/dat/leap/cmd/oldff/leaprc.ff14SB
> > > ----- Source of
> > /home/joao/maindisk/software/amber16/dat/leap/cmd/oldff/leaprc.ff14SB
> done
> > 69c69
> > < log started: Tue Jan 31 20:21:26 2017
> > ---
> > > log started: Tue Jan 31 21:15:45 2017
> > 169c169
> > < Loading parameters:
> > /home/joao/maindisk/software/amber14/dat/leap/parm/parm10.dat
> > ---
> > > Loading parameters:
> > /home/joao/maindisk/software/amber16/dat/leap/parm/parm10.dat
> > 175c175
> > < Loading parameters:
> > /home/joao/maindisk/software/amber14/dat/leap/parm/frcmod.ff14SB
> > ---
> > > Loading parameters:
> > /home/joao/maindisk/software/amber16/dat/leap/parm/frcmod.ff14SB
> > 183c183
> > < Loading library:
> > /home/joao/maindisk/software/amber14/dat/leap/lib/amino12.lib
> > ---
> > > Loading library:
> > /home/joao/maindisk/software/amber16/dat/leap/lib/amino12.lib
> > 213c213
> > < Loading library:
> > /home/joao/maindisk/software/amber14/dat/leap/lib/aminoct12.lib
> > ---
> > > Loading library:
> > /home/joao/maindisk/software/amber16/dat/leap/lib/aminoct12.lib
> > 241c241
> > < Loading library:
> > /home/joao/maindisk/software/amber14/dat/leap/lib/aminont12.lib
> > ---
> > > Loading library:
> > /home/joao/maindisk/software/amber16/dat/leap/lib/aminont12.lib
> > 267c267
> > < Loading library:
> > /home/joao/maindisk/software/amber14/dat/leap/lib/nucleic12.lib
> > ---
> > > Loading library:
> > /home/joao/maindisk/software/amber16/dat/leap/lib/nucleic12.lib
> > 305c305
> > < Loading library:
> > /home/joao/maindisk/software/amber14/dat/leap/lib/atomic_ions.lib
> > ---
> > > Loading library:
> > /home/joao/maindisk/software/amber16/dat/leap/lib/atomic_ions.lib
> > 374c374
> > < Loading library:
> > /home/joao/maindisk/software/amber14/dat/leap/lib/solvents.lib
> > ---
> > > Loading library:
> > /home/joao/maindisk/software/amber16/dat/leap/lib/solvents.lib
> > 376a377,380
> > > Loading: FB3
> > > Loading: FB3BOX
> > > Loading: FB4
> > > Loading: FB4BOX
> > 495a500
> > > >>
> > 498,499c503,504
> > < ----- Source:
> > /home/joao/maindisk/software/amber14/dat/leap/cmd/leaprc.gaff
> > < ----- Source of
> > /home/joao/maindisk/software/amber14/dat/leap/cmd/leaprc.gaff done
> > ---
> > > ----- Source:
> > /home/joao/maindisk/software/amber16/dat/leap/cmd/leaprc.gaff
> > > ----- Source of
> > /home/joao/maindisk/software/amber16/dat/leap/cmd/leaprc.gaff done
> > 501c506
> > < log started: Tue Jan 31 20:21:27 2017
> > ---
> > > log started: Tue Jan 31 21:15:45 2017
> > 589c594
> > < Loading parameters:
> > /home/joao/maindisk/software/amber14/dat/leap/parm/gaff.dat
> > ---
> > > Loading parameters: ./gaff.dat
> > 596c601
> > < Loading parameters:
> > /home/joao/maindisk/software/amber14/dat/leap/parm/frcmod.ionsjc_tip3p
> > ---
> > > Loading parameters:
> > /home/joao/maindisk/software/amber16/dat/leap/parm/frcmod.ionsjc_tip3p
> >
> > If one excludes the differences in the paths, the only difference is in
> the
> > loading of news solvents (I think? from solvents.lib). These shouldn’t
> > affect.
> >
> > The output .crd is the same, no differences. But the output .prmtop files
> > are different.
> >
> > Namely,
> >
> > - there are differences in the POINTERS section, in the 8th and 15th
> > entry, which correspond to the MPHIA (number of dihedrals not
> containing
> > hydrogen) and NPHIA (MPHIA + number of constraint dihedrals). The
> > difference is between 7371 and 7373, with AmberTools16 presenting two
> > more:
> >
> > 7,8c7,8
> > < 7196 17 5555 1670 3625 2269 7454 7371
> > 0 0
> > < 23114 1552 1670 2269 7371 68 160 213
> > 35 1
> > ---
> > > 7196 17 5555 1670 3625 2269 7454 7373
> > 0 0
> > > 23114 1552 1670 2269 7373 68 160 213
> > 35 1
> >
> >
> > - the previously mentioned entry differences also show in
> > DIHEDRALS_WITHOUT_HYDROGEN:
> >
> > 2097 2106 -2115 2121 44
> > 4383 4392 -4401 4407 44
> >
> >
> > - lastly, the RADII section, there are multiple differences, where one
> > radius that is 1.2 in AmberTools15, shows as 1.3 in AmberTools16.
> > Sample of
> > differences:
> >
> > 22541,22542c22542,22543
> > < 1.70000000E+00 1.20000000E+00 1.70000000E+00 1.30000000E+00
> > 1.30000000E+00
> > < 1.30000000E+00 1.70000000E+00 1.20000000E+00 1.20000000E+00
> > 1.70000000E+00
> > ---
> > > 1.70000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
> > 1.30000000E+00
> > > 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00
> > 1.70000000E+00
> >
> > The tleap.in file used was this one:
> >
> > # tleap file generated by amber.build
> > source leaprc.lipid14
> > source leaprc.ff14SB (CHANGED TO oldff/leaprc.ff14SB for AmberTools16)
> > source leaprc.gaff
> >
> > # Loading parameter files
> > loadamberparams frcmod.ionsjc_tip3p
> >
> > # Loading prepi topologies
> >
> > # Loading the system
> > mol = loadpdb input.pdb
> >
> > # Adding disulfide bonds
> > bond mol.22.SG mol.152.SG
> > bond mol.40.SG mol.56.SG
> > bond mol.124.SG mol.225.SG
> > bond mol.131.SG mol.198.SG
> > bond mol.163.SG mol.177.SG
> > bond mol.188.SG mol.212.SG
> >
> > # Writing out the results
> > saveamberparm mol structure.prmtop structure.crd
> >
> > The input.pdb from built from PDB 3PTB.
> >
> > I can share the files that I used and the outputs. Let me know the
> platform
> > that you prefer for receiving the files.
> >
> > Is there any reason for these differences? We are trying to have a smooth
> > transition from AmberTools15 to AmberTools16 and it would be very helpful
> > to have your insight on these. Thank you.
> >
> > Best regards,
> > João
> >
> > --
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Feb 01 2017 - 13:30:02 PST
