i hv several ligands and a receptor, say, 7ligands and 1receptor. now i am preparing .gpf file for all the possible combinations manually using autodock software. but i found that all those .gpf files are similar.
is it that all are same or i am making some mistake?
Hi Anwesh,
Since your receptor/macromolecule is same, you should be using same grid box (Active site/binding site) I suppose. In that case, all your grid.gpf files will look similar except the ligand types may change. May be you can check for difference in ligand type.
Cheers
hello sneha mam, that's what the thing is, despite having different ligands with the same receptor; yet i am getting the same .gpf file for all of them.
Could it be that all your ligands contain the same set of atom types?
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i haven't used AutoDock since 2005 but i think that you don't need to have ligand-specific gpf files: one gpf file for all atom types in the set of ligands is enough.
As Martin quoted,. Gpf files could be same if you have same ligand files
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