Dear Jason,
Yes, I have now been able to test this, and the problem is resolved!
(i.e. with parmed installed from
https://github.com/ParmEd/ParmEd, the FAD
geometry minimised using the chamber-action prmtop is now as expected, not
distorted).
Thank you very much for sorting this out.
Best wishes,
Marc
On 23 November 2016 at 16:47, Jason Swails <jason.swails.gmail.com> wrote:
> Hi Marc,
>
> I've pushed and merged a fix to this issue in the development version of
> GitHub (see https://github.com/ParmEd/ParmEd). Can you check that the fix
> there solves your problem?
>
> Thanks,
> Jason
>
> On Fri, Nov 18, 2016 at 7:49 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > For anyone interested, the problem is that chamber was not converting the
> > improper torsions to radians. The original documentation was a bit
> > misleading, and since the vast majority of all improper phase shifts are
> 0,
> > this was not caught before.
> >
> > All the best,
> > Jason
> >
> > --
> > Jason M. Swails
> >
> > On Nov 18, 2016, at 5:39 PM, Marc van der Kamp <marcvanderkamp.gmail.com
> >
> > wrote:
> >
> > Many thanks for looking into it, Jason.
> > Much appreciated!
> > Marc
> >
> > On 18 Nov 2016 7:45 p.m., "Jason Swails" <jason.swails.gmail.com> wrote:
> >
> > There is definitely something wrong with the improper torsions... I am
> >
> > looking into it and will fix it sometime this weekend. I will post
> updates
> >
> > to the github issue as I find stuff.
> >
> >
> > Thanks,
> >
> > Jason
> >
> >
> > On Thu, Nov 10, 2016 at 10:01 AM, Marc van der Kamp <
> >
> > marcvanderkamp.gmail.com> wrote:
> >
> >
> > Dear all,
> >
> >
> > I have run into a curious problem when performing minimization with a FAD
> >
> > co-factor, based on a Parmed-generated chamber prmtop.
> >
> >
> > Initially, a .psf file was generated with VMD's psfgen using CHARMM-style
> >
> > parameters for FAD.
> >
> > I confirmed that minimization with NAMD of FAD in vacuum, using the .psf
> >
> > and .pdb file is ok.
> >
> > (see min_namd.pdb attached).
> >
> >
> > Then I convert this psf and pdb with Parmed's chamber action (parmed
> >
> > version 2.4.0 from AmberTools16):
> >
> >
> > chamber -top top_all36_prot.rtf -top top_all36_na.rtf -top
> >
> > top_all36_cgenff.rtf -top jp4061522_si_002_mod.txt -param
> >
> > par_all36_prot.prm -param par_all36_cgenff.prm -param
> >
> > par_all36_lipid.prm
> >
> > -param jp4061522_si_003_mod.txt -str toppar_water_ions.str -psf
> >
> > test_fad.psf -crd test_fad.pdb -box bounding
> >
> >
> > parmout test_fad.prmtop test_fad.rst
> >
> >
> > However, when I perform minimization with sander using the resulting
> >
> > test_fad.prmtop and test_fad.rst files, something curious happens:
> >
> > The central structure in the flavine ring distorts in a strange way - In
> >
> > particular, C6A and C4A appear to exchange position, and both the
> >
> > configuration around N5 and N10 is distorted.
> >
> > (see min_test.pdb)
> >
> >
> > I've checked what parmed reports for the bonds of these atoms, and this
> >
> > is
> >
> > all as expected.
> >
> >
> > Is this some strange bug in the writing of the prmtop?
> >
> > I'm attaching an archive that contains the files required to run the
> >
> > above
> >
> > Parmed-command.
> >
> >
> > Thank you in advance for looking into this!
> >
> > Marc
> >
> >
> > _______________________________________________
> >
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> >
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> >
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> >
> >
> >
> >
> >
> > --
> >
> > Jason M. Swails
> >
> > _______________________________________________
> >
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> >
> > AMBER.ambermd.org
> >
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
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> >
> >
>
>
> --
> Jason M. Swails
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Received on Thu Nov 24 2016 - 03:00:04 PST
