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insilichem / ommprotocol

A command line application to launch molecular dynamics simulations with OpenMM
http://ommprotocol.readthedocs.io
GNU Lesser General Public License v3.0
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Box not detected in pdb file (Charmm) #16

Closed Lrolmar closed 4 years ago

Lrolmar commented 4 years ago

Hi there!

I have been trying to perform MD simulations with a .psf and .pdb file, but an error arises that the system is not under periodic boundary conditions. I checked and the water box is properly defined in the .pdb file (in the first line). How can I solve it?

jaimergp commented 4 years ago

Apparently the CharmmPsfFile handlers requires their periodicBoxVectors keyword to be set to the has_box checks are done upon system creation. This is now fixed in latest master and will be in the next patch release. Thanks for the report!

jaimergp commented 4 years ago

v0.1.13 is online at -c insilichem. It can be installed in an existing environment with:

conda install -c conda-forge -c omnia -c insilichem ommprotocol=0.1.13

Take into account that for this fix to be applied, box vectors must be specified explicitly (even using the same file if needed):

topology: helix_wb.psf
positions: helix_wb.pdb
box: helix_wb.pdb  # <<<--- this line is needed
forcefield:
  - top_all36_prot.rtf
  - toppar/toppar_water_ions.str
  - par_all36m_prot.prm