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forlilab / Meeko

Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
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mk_prepare_receptor #77

Open TommyBiomodellingAU opened 8 months ago

TommyBiomodellingAU commented 8 months ago

Is it not possible to use mk_prepare_receptor to prepare a pdb file for flexible docking only and not for reactive docking?

diogomart commented 8 months ago

Yes, use -f or --flexres instead of --reactive_flexres.

TommyBiomodellingAU commented 8 months ago

right, thanks. The actual problem seems to be that mk_prepare_receptor.py does not recognize the terminals of the pdb structures i am using. It just says "amino acid does not match template". It happens with and without ACE/NMA capping as well

diogomart commented 8 months ago

Currently it expect all atom names, including hydrogens, to match the atom names from Amber, and only standard amino acids are supported. So it is very restrictive. The new version that fixes these issues will be released in a few weeks.