Re: [AMBER] mol2 files for FEW

From: David A Case <>
Date: Wed, 1 May 2019 13:50:43 -0400

On Tue, Apr 30, 2019, Zhonghua Xia wrote:

>The atom names in the mol2-file /home/zhonghua/disk/FEW/structs/Lig_ligprep_434.maegz:1.mol2
>are not unique. The atom name C is present at least twice.
>Please ensure that the atom names in the ligand mol2-files are unique.

You need to fix this. Just look at the mol2 file you attached: it has
many atoms named just "C", and many more named "H", etc. One fix is
just to run through antechamber, which will give unique (albeit
arbitrary) atom names:

   antechamber -i PVL_1.mol2 -fi mol2 -o new.mol2 -fo mol2

...hope this helps....dac

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Received on Wed May 01 2019 - 11:00:02 PDT
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