Thanks again for producing such a wonderfully useful tool!
I was wondering if it would be possible to have packmol preserve connectivity information on writing output PDB files. The PDB Specification requires that nonstandard residues (anything but the standard 20 amino acids, 4 RNA and DNA nucleic acids, and water) use the HETATM record and include CONECT records that define connectivity between nonstandard atoms. The reason for this is that there is absolutely no way to infer what the connectivity in the output molecules otherwise.
Is it possible to add a feature that would preserve the molecular connectivity and write the corresponding CONECT records within the output PDB file? Many software packages like OpenMM require this information in order to be able to use the downstream PDB files.
lmiq
commented
4 years ago
Thanks again for producing such a wonderfully useful tool!
I was wondering if it would be possible to have packmol preserve connectivity information on writing output PDB files. The PDB Specification requires that nonstandard residues (anything but the standard 20 amino acids, 4 RNA and DNA nucleic acids, and water) use the
HETATMrecord and includeCONECTrecords that define connectivity between nonstandard atoms. The reason for this is that there is absolutely no way to infer what the connectivity in the output molecules otherwise.Is it possible to add a feature that would preserve the molecular connectivity and write the corresponding
CONECTrecords within the output PDB file? Many software packages like OpenMM require this information in order to be able to use the downstream PDB files.cc: https://github.com/openmm/openmmforcefields/issues/140