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-- 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 >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >>> >> >> >> -- >> Jason M. Swails >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Nov 18 2016 - 17:00:02 PST