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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
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>
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Received on Fri Nov 18 2016 - 15:00:02 PST
