Dear Aldo,
This is very helpful. antechamber is running longer which is a good sign. How did you calculate the charge on molecule? Can you please share?
Many thanks,
Anupam
________________________________
From: Aldo Segura [asegurac666.yahoo.com.mx]
Sent: Friday, December 05, 2014 1:59 PM
To: Anupam Goel; AMBER Mailing List
Subject: Re: [AMBER] error creating mol2 files
Hi Anupan,
Your molecule has -2 charge. Then, you need to provide that information to antechamber by using the -nc flag otherwise it will considerer a neutral molecule.
Try to do this:
antechamber -i your_pdb_file.pdb -fi pdb -o your_output_file.mol2 -fo mol2 -c bcc -nc -2
Good luck,
Aldo
=======================================
Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer 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: Aldo Segura <asegurac666.yahoo.com.mx>; AMBER Mailing List <amber.ambermd.org>
Enviado: Viernes, 5 de diciembre, 2014 13:35:13
Asunto: RE: [AMBER] error creating mol2 files
Yes I am trying to get ligand parameters
________________________________
From: Anupam Goel
Sent: Friday, December 05, 2014 12:34 PM
To: Aldo Segura; AMBER Mailing List
Subject: RE: [AMBER] error creating mol2 files
I am using antechamber -i input.pdb -fi pdb -o output.mol2 -fo mol2 -c bcc -s 2
and the sqm.in file as below (not sure how to control it being overwritten when invoked from antechamber to change tolerance and tightness values)
qm_theory='AM1', grms_tol=0.0002,
tight_p_conv=1, scfconv=1.d-10, qmcharge=0
/
Really appreciate your help.
________________________________
From: Aldo Segura [asegurac666.yahoo.com.mx]
Sent: Friday, December 05, 2014 12:05 PM
To: Anupam Goel; AMBER Mailing List
Subject: Re: [AMBER] error creating mol2 files
Sorry, I mean for antechamber intead of leap.
First of all, what are you trying to do? getting ligand parameters for a simulation?
Best,
Aldo
=======================================
Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer 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: Aldo Segura <asegurac666.yahoo.com.mx>; AMBER Mailing List <amber.ambermd.org>
Enviado: Viernes, 5 de diciembre, 2014 12:16:58
Asunto: RE: [AMBER] error creating mol2 files
Dear Aldo,
What do you mean by Leap settings specifically? Sorry I am new to the MD world.
I start leap and load the ff99SB and GAFF force fields. On loading the molecule and checking unit, Leap shows no charges.
But if that's the problem, what is the way out? From reading about this problem, I came across something called "capping the termini" - is that what I need to do?
Thanks,
Anupam
________________________________________
From: Aldo Segura [asegurac666.yahoo.com.mx<mailto:asegurac666.yahoo.com.mx>]
Sent: Friday, December 05, 2014 10:54 AM
To: AMBER Mailing List
Subject: Re: [AMBER] error creating mol2 files
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<mailto:goelan.uab.edu>>
Para: "amber.ambermd.org<mailto:amber.ambermd.org>" <amber.ambermd.org<mailto: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 - 13:00:03 PST
