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shirtsgroup / InterMol

Conversion tool for molecular simulations
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InterMol unable to recognize when the molecule tag for each atom at least when converting to gromacs files #350

Open JoshuaSBrown opened 5 years ago

JoshuaSBrown commented 5 years ago

E.g. Here is a section from a lammps.data file that is in the Atoms section notice that the molecular tag changes at atoms 517 to 518. 

      513         1       10  -0.02660800   -18.795860   -17.866504     6.424540 #    HC
      514         1        8  -0.33129100   -18.695024   -15.769852     6.844219 #    CT
      515         1       10   0.07227600   -17.793134   -15.818433     7.454617 #    HC
      516         1       10   0.07227600   -18.701067   -14.816105     6.317202 #    HC
      517         1       10   0.08113100   -19.555138   -15.794549     7.513446 #    HC
      518         2        1   0.20660700   -43.466510    24.465123   -45.923757 #    CB
      519         2        1  -0.17133700   -44.295471    23.901868   -44.989479 #    CB
      520         2        2   0.04657400   -43.113915    23.781029   -47.097746 #    CA
      521         2        3  -0.27708900   -43.052059    25.775495   -45.552924 #    CS
      522         2        2   0.30839100   -44.801953    22.606565   -45.175180 #    CA

And here is the output from the converted gromacs file created using intermol:

    1R01  A201   513  -1.879586000000  -1.786650400000   0.642454000000
    1R01  A202   514  -1.869502400000  -1.576985200000   0.684421900000
    1R01  A203   515  -1.779313400000  -1.581843300000   0.745461700000
    1R01  A204   516  -1.870106700000  -1.481610500000   0.631720200000
    1R01  A205   517  -1.955513800000  -1.579454900000   0.751344600000
    1R01  A206   518  -4.346651000000   2.446512300000  -4.592375700000
    1R01  A207   519  -4.429547100000   2.390186800000  -4.498947900000
    1R01  A208   520  -4.311391500000   2.378102900000  -4.709774600000
    1R01  A209   521  -4.305205900000   2.577549500000  -4.555292400000
    1R01  A20a   522  -4.480195300000   2.260656500000  -4.517518000000

Notice that the residue number has not been changed to indicate that the atoms are on a separate molecule. They are all considered to be on residue 1.

ctk3b commented 5 years ago

It's been a while but at a quick glance, I do not think we ever got around to implementing this in the LAMMPS parser: https://github.com/shirtsgroup/InterMol/blob/master/intermol/lammps/lammps_parser.py#L401

https://github.com/shirtsgroup/InterMol/blob/master/intermol/lammps/lammps_parser.py#L394

JoshuaSBrown commented 5 years ago

Just a heads up, I have just been made aware that there is this package that provides file parsing capabilities for several molecular dynamics file types. You might already be aware.

https://www.mdanalysis.org/docs/documentation_pages/topology/init.html

And I'll see if I can fix the issue.

ctk3b commented 5 years ago

Last I checked MDAnalysis did not read or convert forcefield parameters but it's been a while since I tried it.

The other package that we've been involved in is https://github.com/ParmEd/ParmEd which does perform full forcefield parameter conversions but does not yet support LAMMPS. ParmEd is actually how InterMol operates on Amber files: https://github.com/shirtsgroup/InterMol/blob/master/intermol/convert.py#L641