Hi David,
I am currently using Smina to perform docking calculations of proteins with metalloligands.
In order to simulate coordination bonds I need to include gaussian functions to the scoring between certain types of atoms (e.g. N aromatics of Histamine). For doing that what I am currently doing is defining these atoms as another element and changing its properties with --custom_atoms. As you can see it is not the most desirable way to do it.
My aim is to define a new type of atom (e.g. N.ar) with --custom_atom. The problem is that I don't know how to call it in the .pdb or .mol2 file to make it recognisable for Smina. Any suggestion to this problem?
Thank you so much and congratulations for this incredible software.
Fernando Davó Miralles.
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Unfortunately, you are stuck with the built-in types (although their parameters can be changed) and there is no aromatic nitrogen type. There are four nitrogen types:
NitrogenXSDonor (N AD4 type with a hydrogen attached)
Nitrogen (N AD4 type without a hydrogen attached)
NitrogenXSDonorAcceptor (NA AD4 type with a hydrogen attached)
NitrogenXSAcceptor (NA AD4 type without a hydrogen attached)
You can likely overload one of these if you are providing a PDBQT as an input.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi David,
I am currently using Smina to perform docking calculations of proteins with metalloligands.
In order to simulate coordination bonds I need to include gaussian functions to the scoring between certain types of atoms (e.g. N aromatics of Histamine). For doing that what I am currently doing is defining these atoms as another element and changing its properties with --custom_atoms. As you can see it is not the most desirable way to do it.
My aim is to define a new type of atom (e.g. N.ar) with --custom_atom. The problem is that I don't know how to call it in the .pdb or .mol2 file to make it recognisable for Smina. Any suggestion to this problem?
Thank you so much and congratulations for this incredible software.
Fernando Davó Miralles.
Unfortunately, you are stuck with the built-in types (although their parameters can be changed) and there is no aromatic nitrogen type. There are four nitrogen types:
NitrogenXSDonor (N AD4 type with a hydrogen attached)
Nitrogen (N AD4 type without a hydrogen attached)
NitrogenXSDonorAcceptor (NA AD4 type with a hydrogen attached)
NitrogenXSAcceptor (NA AD4 type without a hydrogen attached)
You can likely overload one of these if you are providing a PDBQT as an input.