Re: [AMBER] stopping antechamber

From: <zmatovic.kg.ac.rs>
Date: Fri, 28 Jun 2019 21:41:51 +0200

Hi Andrew,
You should be just more patient, AM1 needs more iteration for your molecule
to converge...find in attachment lig.mol2 file written with gaff2 after
antechamber.

Zoran

-----Original Message-----
From: Andrew Bostick <andrew.bostick1.gmail.com>
Sent: Friday, June 28, 2019 5:51 PM
To: amber.ambermd.org
Subject: [AMBER] stopping antechamber

Hi all, stopping antechamber

I am using antechamber for my ligand molecule. After using following
command,

antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc -s 2

I encountered with following lines for long time:
---------------------------------------------------------------------------- 
----
Welcome to antechamber 17.3: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
   Status: pass
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded
      for those not bond
   Status: pass
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.
Info: Total number of electrons: 520; net charge: 0
Running: /home/katouzian/Desktop/Ambertools/AmberTools18/amber18/bin/sqm -O
-i sqm.in -o sqm.out
----------------------------------------------------------------------------
----
lig.mol2 file was not created. It seems that the antechamber has been
stopped.
How to resolve that?
lig.pdb file in in following link:
https://1drv.ms/f/s!AveJH4Y30cH0rEU08meMh0EEfQde
Best,
Andrew
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Received on Fri Jun 28 2019 - 13:00:03 PDT
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