[gmx-users] best force field for small proteins
Smith, Micholas D.
smithmd at ornl.gov
Thu Oct 18 15:07:05 CEST 2018
There isn't really a good answer to that question without more information.
If you want all-atom then the standard choices are:
OPLS-AA (variants exist)
CHARMM (variants exist)
AMBER (variants exist)
If your protein has a lot of disorder, traditionally, some flavor of AMBER or OPLS would be good choice, if it is a nice folded structure then CHARMM is also a fine choice.
Since you have a ligand you will need to consider which force-field will also have parameters that will be reliable for the ligand. CHARMM has cgenff for ligands (I would suggest using the CHARMM-GUI to get these parameters since it has a nice interface), Amber has gaff (not my area of expertise for ligands), and OPLS is pretty much tinker-toys, so you can generate ligand parameters directly from a nice little webserver provided by the jorgensen group (LigParGen).
Hope that helps. There are some papers comparing the force-fields for a number of proteins/peptides floating around also (I would suggest checking JCIM and JCTC as they these comparisons typically show up in these journals)
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ali khamoushi <khamuoshia at gmail.com>
Sent: Thursday, October 18, 2018 8:54 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] best force field for small proteins
Hello everyone. I wanna to use MD for a protein with about 50 Amino acid
and without ligand. what are the best force fields for this purpose?
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