Re: [AMBER] error creating mol2 files

From: Aldo Segura <asegurac666.yahoo.com.mx>
Date: Fri, 5 Dec 2014 16:54:04 +0000 (UTC)

Hi,
It would be great if you can provide more information about this issue. For example, what parameters did you use for leap?It seems that the problem is related with the charges on your molecule. Maybe you're running leap assuming that you have a neutral molecule, but I think yours have some charge (ADP).
Best,
Aldo 
 =======================================
Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer BiologyCancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
=========================================
      De: Anupam Goel <goelan.uab.edu>
 Para: "amber.ambermd.org" <amber.ambermd.org>
 Enviado: Viernes, 5 de diciembre, 2014 11:26:13
 Asunto: [AMBER] error creating mol2 files
   

Dear Sir/Madam,

I am using antechamber in AMBER to calculate point charges of ADP-ribose and make a mol2 file for it. However, I keep getting this error:

Error: cannot run "/usr/local/amber12/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

and the sqm.out reports as follows:

QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after  1000 steps.
QMMM: E =  -0.1469E+07 DeltaE =  0.3107E+00 DeltaP =  0.4433E-01
QMMM: Smallest DeltaE =  -0.4193E-03 DeltaP =  0.6142E-02 Step =    453

I have been struggling with this for sometime now. Can you tell me what is it that I am doing wrong? Do I need to upgrade from Amber 12 to 14?

Many thanks,
Anupam
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Received on Fri Dec 05 2014 - 09:00:03 PST
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