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 - 14:00:02 PDT
