Re: [AMBER] SQM error while preparing ATP with antechamber

From: David A Case <>
Date: Wed, 6 Aug 2014 09:04:30 -0700

On Wed, Aug 06, 2014, Hirdesh Kumar wrote:

> I am trying to prepare the ATP molecule (attached) using antechamber. I
> added hydrogen using xleap and the used antechamber to prepare it..
> With following commands:
> *antechamber -i ATP_H.pdb -fi pdb -o -fo ac -c bcc -nc -4*
> I got this error:
> *Running: /opt/bwgrid/chem/amber/12/bin/sqm -O -i <> -o
> sqm.out*
> *Error: cannot run "/opt/bwgrid/chem/amber/12/bin/sqm -O -i
> <> -o sqm.out" of bcc() in charge.c properly, exit...*

As the sqm.out file shows, the program failed to acheive self-consistency,
which can often be a problem with highly charged anions. You might try the
suggestions in Note 6 on p. 262 of the Amber manual.

A better suggestion is to use the ATP parameters available here:

(Look under "cofactors"; input files and references to the original papers are


AMBER mailing list
Received on Wed Aug 06 2014 - 09:30:02 PDT
Custom Search