Re: [AMBER] antechamber parametrization of desoxycorticosterone

From: Jason Swails <>
Date: Thu, 21 Aug 2014 09:26:13 -0400

On Thu, 2014-08-21 at 15:59 +0300, BATUHAN KAV wrote:
> Dear All,
> I am trying to parametrize desoxycorticosterone (C_21-H_30-O_3) with
> antechamber. Then I will simulate this molecule along with the protein.
> Using antechamber, I entered this command
> antechamber -i des.pdb -fi pdb -o des.mol2 -fo mol2 -c bcc -s 2
> but I ended up with
> Error: cannot run "/home/peptid/Desktop/master/software/amber14/bin/sqm -O
> -i -o sqm.out" of bcc() in charge.c properly, exit

In response to the same question you asked yesterday, Dave told you that
you needed all hydrogen atoms added to your PDB file. We also told you
the problem with pasting a PDB file directly in an email.

> and tail of sqm.out file is
> QMMM: Unable to achieve self consistency to the tolerances specified
> QMMM: No convergence in SCF after 1000 steps.
> QMMM: E = -0.4929E+06 DeltaE = 0.1319E+01 DeltaP = 0.4179E-01
> QMMM: Smallest DeltaE = 0.2006E-04 DeltaP = 0.2178E-02 Step = 94

You clearly need to add hydrogen atoms. You shouldn't expect a sensible
wavefunction from any QM program without all of the atoms and electrons

If you still get a problem even after you've fixed your PDB file, try
putting the error message into Google and see if you can find any
helpful advice before emailing the list -- you will probably find your
answer faster that way.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Aug 21 2014 - 06:30:06 PDT
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