Using the pdb2gmx module, I separately parameterized two proteins (polymers), I used the topologies of both and joined them in a single topol.top file. I have minimized the energy and the gromacs preprocessor (grommp) does not warn about any error in the simulation, however when executing the mdrun module, in the last line I get the message: "WARNING: There are no atom pairs for dispersion correction"
Is this something to worry about or is it related to the gromacs version? If I have already taken steps to equilibrate the system, should they not be considered valid?
CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins
Jing Huang,1 Sarah Rauscher,2 Grzegorz Nawrocki,3 Ting Ran,1 Michael Feig,3 Bert L. de Groot,2 Helmut Grubmüller,2 and Alexander D. MacKerell, Jr.1,*
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
2Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
3Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
*Email: ude.dnalyramu.xr@erekcamaAbstract
The all-atom additive CHARMM36 protein force field is widely used in molecular modeling and simulations. We present its refinement, CHARMM36m (http://mackerell.umaryland.edu/charmm_ff.shtml), with improved accuracy in generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins.
There is increasing interest in intrinsically disordered peptides and proteins (IDPs) due to their abundance and functional importance in eukaryotes, as well as their association with various human disorders ranging from cancer to neurodegenerative diseases. Rather than folding into a single, well-defined three-dimensional structure, an IDP fluctuates between an ensemble of interconverting conformational states, which allows some IDPs to interact with several different binding partners, thereby functioning in protein-protein interaction networks.1 Experimental characterization of conformational ensembles of IDPs is challenging; assistance from computer simulations is often needed, as the number of degrees of freedom of an IDP far exceed the number of available experimental observables.2 Recent advances in hardware and software allow molecular simulations to reach relevant timescales for sampling IDP conformations, but a major limiting factor lies in the accuracy of their underlying models, typically empirical force fields (FFs).3 Protein FFs were mostly developed targeting folded proteins and their accuracy in modeling IDPs needs to be scrutinized and improved
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