[AMBER] Assigning am1-bcc charges to a whole library of ligands

From: Liao <liaojunzhuo.aliyun.com>
Date: Sat, 26 Oct 2019 21:31:56 +0800

Dear Fellow Users,

I’m trying to assign am1-bcc charges to a whole library of virtual screening molecules, for docking.

Are there any good ways to assign the charges at once, by loading the whole library of ligand molecules and let the program do the rest?
I’ve tried to load the ligands (pdbs or mol2s) into chimera, and it almost works, with the exception that it crashes when running addcharge.

I wrote a simple python script to call antechamber from the command line and load each and every single ligand for charge assignment and saving each as a mol2. It works with one caveat: the net charge parameter for each ligand is different, it can be -1, 0, or 1 etc (the -nc parameter), but I can only put in one value. Chimera automatically recognizes each (the user just needs to confirm them, all together). In MOE with mopac the user does not need to specify the net charge and the net charge is automatic.

I know some databases have partial charges assigned, but many don’t. Any insight on this issue? This seems to be a common enough thing to be done, have people just been using Chimera but without the crashes?


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Received on Sat Oct 26 2019 - 07:00:01 PDT
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