Re: [AMBER] Energy Minimization of a Complex

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Sun, 7 Feb 2010 19:53:49 -0600

Hi Muhammad,

The problem is that the mol2 format that is produced by antechamber has atom
types that are appropriate for input into the leap program only.

In order to produce a mol2 file using antechamber that is produces the
"typical" Sybyl mol2 atom types, you need to change the output flag:

"... to display molecules properly
in software packages other than LEaP and gleap, one needs to assign atom
types using the '-at sybyl' flag rather than using the default gaff atom
types. "

--from the Ambertools manual.

Good luck!

Dean

-- 
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
> From: MUHAMMAD IMTIA SHAFIQ <imtiazshafiq.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Sun, 7 Feb 2010 18:22:57 -0600
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Energy Minimization of a Complex
> 
> Dear All,
> 
> 
> I want to run mmpbsa calculations of a protein docked with a small organic
> ligand. I have parametrize the ligand as follow
> 
> 
> 1. Converted mol file (originally created in hyperchem)  to gaussian input
> file
> 
> 2. Obtained Gaussian output file after Gaussian calculations.
> 
> 3. run the antechamber and obtained a mole2 file from Gaussian output .
> 
> 4. run the parmchk  and obtained the frcmod file
> 
> 5. Finally I have created prmtop and inpcrd files for ligand
> 
> 
> I can run simulation on ligand and on both protein alone. Now I wish to run
> simulations with the protein ligand complex. I tried docking ligand mole2
> (file obtained with antechamber from Gaussian output) with protein using Gold
> but Gold do not recognise this mole2 file. I tried opening this mole2 in
> hyperchem and unable to open this file as it complain not in correct format.
> 
> However I am able to dock original mol file with protein. But I can load this
> mol file with frcmod file obtained with mole2 file.
> 
> Please suggest me at this stage how I can make a complex which can be used
> with amber for mmpbsa.
> 
> 
> Regards
> Imtiaz 
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Received on Sun Feb 07 2010 - 18:00:02 PST