On Mon, May 05, 2025, Kehinde Idowu via AMBER wrote:
>Dear All,I am running antechamber on a small molecule to generate LIG.mol2
>file using this script (antechamber -i lig.mol2 -fi mol2 -o LIG.mol2 -fo
>mol2 -j 4 -at gaff -c bcc -nc 0) but i have consistently got this error
>message.kindly, advise on what to do.thanks.
>Info: acdoctor mode is on: check and diagnose problems in the input file.Info: The atom type is set to gaff; the options available to the -at flag are gaff, gaff2, amber, bcc, and sybyl.
>-- Check Format for mol2 File -- Status: pass-- Check Unusual Elements -- Status: pass-- Check Open Valences -- Status: pass-- Check Geometry -- for those bonded for those not bonded Status: pass-- Check Weird Bonds --/apps/amber/22/bin/wrapped_progs/antechamber: Fatal Error!Weird atomic valence (5) for atom (ID: 2, Name: C1). Possible open valence.
First, check your lig.mol2 file visually, especially around atom C1. Does
it look like a chemically-correct ground state?
If you can't see the problem, please post the lig.mol2 file for others to
look at.
...dac
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Received on Tue May 06 2025 - 06:30:02 PDT
