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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>
>
>
>
>
> --
>
> Jason M. Swails
>
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--
Jason M. Swails
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Received on Wed Nov 23 2016 - 09:00:04 PST
