Jorge Roel comments

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                                            Jorge Roel

Try to dock AMP (adenosine monophosphate) to a ssDNA

Hi @taoliu032 , We've been looking into this and have parametrized AMP. Preliminary tests show that simulation finishes without issues and poses are correctly generated. However, we can not judge...

Try to dock AMP (adenosine monophosphate) to a ssDNA

@taoliu032 Did you have the chance to try it out? I will close the issue for now but feel free to reopen it if needed.

Membrane atoms not being recognised (BJ)

Hi @wjs20 Problem arises from the last column (Bj). If you replace it by P (or any other real atom I believe C,N,O ), it should work.

Membrane atoms not being recognised (BJ)

Looks like there's still an issue. Try to remove all lightdock_* init/ and swarm_*/ and try again the setup. If error persists, please upload your receptor and ligand pdbs and...

Membrane atoms not being recognised (BJ)

So it acts in 2 steps: First, as you mention, as a filter for the generation of the swarms so that only swarms at the region of interest will be...