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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Received on Tue Oct 16 2018 - 14:00:03 PDT
