Re: [AMBER] Stuck somewhere using antechamber

From: David A Case <>
Date: Thu, 7 Jul 2016 08:40:13 -0400

On Wed, Jul 06, 2016, Xiaoyu Wang wrote:
> I was using antechamber in the toolkit to generate force field and
> connectivity. Everything seems to be okay but it just got stuck
> somewhere on running sqm without any error. I have checked all the file
> it dumped out, but I did not find any error. It is a large molecule
> with 972 atoms. So is this the reason? Here, I attach the pdb file. Can
> anyone help me with this?

As Hai said, this is an enormous molecule. Remember that sqm is (by default)
trying to do a *geometry minimization* on this system, which may never
converge. You could try setting maxcyc=0 in the file, and see if you
can get a single point energy to work. (Use the -ek option in antechamber
if you wish to replace the default sqm options for bcc charges with your own.)


AMBER mailing list
Received on Thu Jul 07 2016 - 06:00:02 PDT
Custom Search