Hi Wes,
This was indeed a bug: https://github.com/ParmEd/ParmEd/issues/756
I fixed it back in June, but no bugfix has been released for AmberTools 18
(yet).
Try updating to the latest version of ParmEd from GitHub and see if that
works.
Also, when you do try to apply this to CHARMM, you may have to add the
CHARMM PSF files directly within ParmEd and then convert the result to an
Amber topology file. The "+" operator may not work on two Amber topology
files that have NBFIX terms.
Good luck,
Jason
On Tue, Oct 16, 2018 at 4:43 PM Wesley Michael Botello-Smith <
wmsmith.uci.edu> wrote:
> Forgot to mention, I am using amber18.
>
> On Tue, Oct 16, 2018 at 1:35 PM Wesley Michael Botello-Smith <
> wmsmith.uci.edu> wrote:
>
> > Hello all,
> > I am trying to use the python api for parmed to merge two separate parm7
> > files into a single file that can then be fed to parmed to perform
> timerge.
> >
> > What I need is to find a way to use parmed python api to combine two
> parm7
> > files such that they can be fed to command line parmed and have timerge
> run
> > on them.
> > This is normally accomplished by leap followed by parmed, but since I
> want
> > to apply this to a system parameterized using CHARMM36 forcefield (via
> > charmm-gui) that is not an option here because leap will not generate
> > CHARMM forcefield topologies.
> > Thus my strategy is to use parmed to merge the parm7 files directly.
> > To start with, however, I will work with AMBER forcefield parm7 files and
> > see if I can get that to work before tackling the CHARMM forcefield case.
> >
> > I am currently working on a simple test case, but the end goal is to
> > extend this to parm7 files generated from charmm psf topologies (since
> leap
> > cannot do this for me)
> > To start i use leap to build ala.parm7 and ser.parm7
> > E.g.
> > testALA = sequence {ALA}; saveamberparm testALA ala.leap.parm7
> > ala.leap.rst7 ... etc
> >
> > I also use leap to build the combined topology ala_ser.parm7 to serve as
> a
> > test case to make sure I get equivalent results from parmed using
> > testALASER = combine {testALA testSER}
> > saveamberparm testALASER ala_ser.leap.parm7 ala_ser.leap.rst7
> >
> > Then using jupyter notebook
> > import parmed as pmd
> > alaStruc=pmd.load_file('ala.parm7')
> > serStruc=pmd.load_file('ser.parm7')
> > ala_ser=alaStruc+serStruc
> > ala_ser.save('ala_ser.pmd.parm7')
> >
> > Unfortunately, ala_ser.pmd.parm7 cannot be opened by parmed
> > (ala_ser.leap.parm7 can and can be merged with timerge).
> >
> > looking at the two parm7 results notice several areas that are different.
> > Most conspicuously, the NONBONDED and LJ relevant flages. E.g:
> >
> > ala_ser.leap.parm7
> > %FLAG NONBONDED_PARM_INDEX
> > %FORMAT(10I8)
> > 1 2 4 7 11 16 22 29 37
> > 2
> > 3 5 8 12 17 23 30 38 4
> > 5
> > 6 9 13 18 24 31 39 7 8
> > 9
> > 10 14 19 25 32 40 11 12 13
> > 14
> > 15 20 26 33 41 16 17 18 19
> > 20
> > 21 27 34 42 22 23 24 25 26
> > 27
> > 28 35 43 29 30 31 32 33 34
> > 35
> > 36 44 37 38 39 40 41 42 43
> > 44
> > 45
> >
> > ala_ser.pmd.parm7
> > %FLAG NONBONDED_PARM_INDEX
> > %FORMAT(10I8)
> > 1 2 4 7 11 16 22 2 3
> > 5
> > 8 12 17 23 4 5 6 9 13
> > 18
> > 24 7 8 9 10 14 19 25 11
> > 12
> > 13 14 15 20 26 16 17 18 19
> > 20
> > 21 27 22 23 24 25 26 27 28
> >
> >
> >
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>
--
Jason M. Swails
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Received on Fri Oct 19 2018 - 12:00:02 PDT
