Re: [AMBER] Problem with Parmed-generated chamber prmtop

From: Jason Swails <>
Date: Fri, 18 Nov 2016 14:45:19 -0500

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.


On Thu, Nov 10, 2016 at 10:01 AM, Marc van der Kamp <> 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

Jason M. Swails
AMBER mailing list
Received on Fri Nov 18 2016 - 12:00:03 PST
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