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UCL-CCS / BAC2

A tool for the automation of molecular simulations using multiple engines, focusing on binding affinity calculations
Apache License 2.0
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Obtain information for building from PDB header #65

Open dww100 opened 6 years ago

dww100 commented 6 years ago

In line with the design outline we need to get information out of a PDB file in order to use in system building.

We have decided to base the workflow on ParmEd. For information we definitely need I will start issue in the ParmEd fork issue tracker and link here. Discuss things you think need to be added below and if you add a relevant issue in ParmEd mention here please.

A full list of PDB records is available here but we probably only need a subset of this information.

Definitely need:

BIOMT UCL-CCS/ParmEd#1 SEQRES UCL-CCS/ParmEd#2 SSBOND UCL-CCS/ParmEd#3

Maybe useful: Missing atom lists Missing residue lists HET information (HET, HETNAM, FORMUL)

dww100 commented 5 years ago

Header reader code now in BAC - however only looks for BIOMT and SEQRES for now. Part of general move to use ParmEd as a library 'as is' and bring functionality into BAC.

ParmEd appears to do a good job of detecting disulphide bonds and putting in bonds list. We should make use of this.