Can Hbind be extended to deal with larger proteins and ligands?

[yakomaxa]

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.

[rasbt]

Hi there, glad to hear that you find it generally useful. In order to fix these issues, I believe you just have to increase the respective numbers here (https://github.com/rasbt/Hbind/blob/e0f8beeb30672af4aff1d2612678283e49961a76/src/hbind/inc/defs.h) and recompile it.

[yakomaxa]

Hi, rasbt. Thank you for your response and suggestions on what to modify. I tried your suggestions and now hbind successfully detects h-bonds between large peptides and proteins!

A note to remember the detail: I needed to remove all the o.file before recompilation. Unless removing them, weird Segfault occurs. I have'nt check the upper-limit of these parameters defined in def.h, but

MAX_PDB_ATOMS 80000 MAX_PDB_RESIDUES 10000 MAX_NUMBER_OF_MOL2_ATOMS 10000 MAX_NUMBER_OF_MOL2_BONDS 10000 MAX_NUMBER_OF_FLEXIBLE_BONDS 10000 MAX_SUBSTS 1000

seems enough for my purpose.

Thank you very much for your support.

[rasbt]

Awesome, glad to hear you got it to work! Let me keep this issue open in case others have similar questions!