Hello,
Basically, Antechamber is for classify atom and bond types ,assign charges and to estimate force field parameters that are missing in the force field that you will be using. It depends how you want to calculate the charge. Since you do not have gaussian, you can calculate the charges in GAMESS program if you want and directly use that output in antechamber. Now in GAMESS I do not remember how many types of charge calculations are present at now. You can give it a try. GAMESS is a free program.
Regarding Am1-bcc method it is a method for calculating charge, it is the default method in antechamber(probably). Now if your system requires a good description of charge then this method is not at all OK since it is a semiempirical method for computing the charge.
Hope this will help you.
Best
Shouryo.
From: SUBHASMITA MAHAPATRA MAHAPATRA <phd2101271009.iiti.ac.in>
Date: Wednesday, 17 July 2024 at 20:10
To: Ghose Shouryo <Shouryo.Ghose.uliege.be>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] running tleap for complex having covalent bond between protein and ligand
Thank you for your response.
I would like to know if I could use antechamber for this purpose, as it uses the same am1-bcc method. I made a pdb with the serine and ligand combined. Then, run antechamber followed by parmchk2 to produce .frcmod files. I would like to know if this method is okay or if I should go for charge calculation separately.
Kindly help in this regard.
Thank you
On Wed, Jul 17, 2024 at 4:04 PM Ghose Shouryo <Shouryo.Ghose.uliege.be<mailto:Shouryo.Ghose.uliege.be>> wrote:
Hello,
You can user the Amber’s QUICK program to generate charges rather than resp say am1 or bcc. This does not require Gaussian..
Best
Shouryo
From: SUBHASMITA MAHAPATRA MAHAPATRA via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>>
Date: Wednesday, 17 July 2024 at 12:32
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: [AMBER] running tleap for complex having covalent bond between protein and ligand
Hi,
I am running tleap for a complex pdb with a covalent bond between SER46 of
protein and CAH atom of ligand. I am following this tutorial:
https://ambermd.org/tutorials/advanced/tutorial1_adv/. However, I am stuck
with the RESP charge calculation as I don't have a license for Gaussian.
Also, I would like to know how to generate the .frcmod file.
Kindly help me in this regard.
Thank you
--
*Yours Sincerely*
*Subhasmita Mahapatra*
*Ph.D. Scholar (PMRF)*
*Computational Biophysics Group*
*Department of Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*Madhya Pradesh, India (453552)*
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Yours Sincerely
Subhasmita Mahapatra
Ph.D. Scholar (PMRF)
Computational Biophysics Group
Department of Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
Madhya Pradesh, India (453552)
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Received on Wed Jul 17 2024 - 11:30:03 PDT
