ADL: AGFR: How to add new atom types

Stephen P. Molnar s.molnar at sbcglobal.net
Wed Dec 23 10:49:51 PST 2020


I do a bit of Python coding and wold be glad to help.

On 12/23/2020 12:46 PM, Michel Sanner wrote:
> Hello
>
> 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
>
> -Michel
>
> From: <autodock-bounces at scripps.edu> on behalf of longorefisher <matthew.fisher at stcatz.ox.ac.uk>
> Reply-To: "autodock at scripps.edu" <autodock at scripps.edu>
> Date: Tuesday, December 22, 2020 at 9:54 AM
> To: "autodock at scripps.edu" <autodock at scripps.edu>
> 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?
>
> Thanks,
> Matthew
>
>
>
> --
> Sent from: http://autodock.1369657.n2.nabble.com/
>
>
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-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1




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