ADL: AGFR: How to add new atom types

Michel Sanner sanner at
Wed Dec 23 09:46:49 PST 2020


The software component ADFRcc underlying AGFR and ADFR and implementing the AutoDock4 scoring function supports extending the built AD4 parameters. However, this functionality is not currently expose to the command line and would require (probably small software modifications). If have some familiarity with Python code I could probably provide you with patch files to allow to specify a parameter file on the agfr and afr command line.
If it works I would include that in the next release of the software


From: <autodock-bounces at> on behalf of longorefisher <matthew.fisher at>
Reply-To: "autodock at" <autodock at>
Date: Tuesday, December 22, 2020 at 9:54 AM
To: "autodock at" <autodock at>
Subject: ADL: AGFR: How to add new atom types

Hi all,

When using AGFR, is there any way to incorporate new atom types? With
Autodock 4; I know I would firstly add the parameters to AD4_parameters.dat
file. Then I would add "parameter_file AD4_parameters.dat" to both the GPF
and DPF when running autogrid4. However, because AGFR automatically calls
autogrid I can't do that. Any ideas on how to add these atom types?


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