Hi Karl,
Thank you for the direction. I already computed partial atomic charges using B3LYP/6-31G** and created lib files
following the tutorial A1: old-advanced version (in which lib files for modified MET and HIS residues were created).
But I would like to try Wolf2Pack as well.
Thanks again,
Senthil Natesan
________________________________
From: Karl N. Kirschner <kkirsch.scai.fraunhofer.de>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, May 21, 2013 3:17 AM
Subject: Re: [AMBER] force field parameters for acetylated lysine
Hello Senthil,
I haven't any experience with the force field published in the Lui and Duan paper you mentioned. However reading the paper, it appears to have developed partial atomic charges for the modified residue, while using existing parameters from the ff03 force field (i.e. Duan et al J. Comput.Chem., 24 (2003), pp. 1999-2012). The partial atomic charges for both studies were developed using B3LYP/cc-pvTZ//HF/6-31G** with a QM continuum solvent model. These charge computations are unique and apply on for the use of this force field - that is, I would not recommend mixing this charge set with a different protein force field (e.g. parm99SB). Other than that, I am not sure how well they performed. Perhaps a citation search of these two papers will provide some insight.
Alternatively, you could also generate partial atomic charges that are compatible with other force field (e.g. parm99SB) using the R.E.D. program. You can check existing or missing internal coordinate parameters for parm99SB using Wolf2Pack, by looking a analogous molecules within its database that have the same internal coordinate.
Cheers,
Karl
----- Original Message -----
From: "Senthil Natesan" <sen.natesan.yahoo.com>
To: amber.ambermd.org
Sent: Friday, May 17, 2013 8:03:52 PM
Subject: [AMBER] force field parameters for acetylated lysine
Dear Amber Users,
I am simulating a peptide with acetylated-lysine residue and looking for its force field parameters. I went through some old posts, and it seems that people suggested to refer the following paper by Dr. Duan:Biophysical
Journal (vol 94, pages 4579-4585) , which cross references to old paper (J.
Comput.Chem., 24 (2003), pp. 1999-2012.
Does anyone have simulated the residue (acetylated lysine) recently and have parameter files ready to share ?
Thanks in advance,
Senthil Natesan
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Received on Tue May 21 2013 - 06:30:02 PDT
