Dear @rasbt,
I'm a bioinformatics researcher and currently trying to use Hbind in my research.
Thank you for developing a very useful tool. I'm currently working on small protein-peptide complexes and using Hbind to analyze their hydrogen bonding network (between proteins and binders). For such small complexes, Hbind works excellently.
Then, I'm planning to extend my work to some large proteins/peptide complexes. When executing Hbind for such complexes, I get error/warning like:
FATAL ERROR: more than MAX_PDB_RESIDUES residues (read_pdb)
for large proteins,
and
WARNING: number of atoms is greater than MAX_NUMBER_OF_MOL2_ATOMS (ligand2.mol2) (read_mol2)
Reading of ligand2.mol2: failed
for large ligand peptides (it's nearly a protein)
Do you have any ideas how to overcome this?
Maybe, such large molecules are out of scope of this software, but any suggestions or workaround will be appreciated because Hbind offers most promising/suitable algorithms for my purposes.
Thank you in advance.
Dear @rasbt,
I'm a bioinformatics researcher and currently trying to use Hbind in my research.
Thank you for developing a very useful tool. I'm currently working on small protein-peptide complexes and using Hbind to analyze their hydrogen bonding network (between proteins and binders). For such small complexes, Hbind works excellently.
Then, I'm planning to extend my work to some large proteins/peptide complexes. When executing Hbind for such complexes, I get error/warning like:
FATAL ERROR: more than MAX_PDB_RESIDUES residues (read_pdb)for large proteins,
and
WARNING: number of atoms is greater than MAX_NUMBER_OF_MOL2_ATOMS (ligand2.mol2) (read_mol2)Reading of ligand2.mol2: failedfor large ligand peptides (it's nearly a protein)
Do you have any ideas how to overcome this?
Maybe, such large molecules are out of scope of this software, but any suggestions or workaround will be appreciated because Hbind offers most promising/suitable algorithms for my purposes.
Thank you in advance.