[gmx-users] Re: simulate a substrate-bound enzyme

Mauricio Pablo Sica msica at unq.edu.ar
Fri Apr 13 14:10:24 CEST 2007

> hello,everyone
> I am new to gromacs. I am studing gromacs following the Tutorial for
> Drug -
> Enzyme Complex,which was written by John E.Kerrigan,Ph.D. In the
> Tutorial, they
> simulated a ligand-protein system, and they stripped the
> drug,parameterized it
> using the PRODRG2 server. 
> Now,I want to simulate a substrate-bound enzyme,and the drug has been
> bound with
> enzyme(there is a bond between them). How can I parameterize the drug?
> If I
> stripped the drug, how can I parameterize the bond between the drug and
> the
> enzyme?

Surely you know what covalent bond you need to make. Then you should:
1. add the ligand as another residue in your  'topol.top'
2. in your 'topol.top', add in the following items the appropriate 
parameters that correspond to the new covalent bond:

[ bonds ]
[ pairs ]
[ angles ]
[ dihedrals ]
[ dihedrals ]

Depending the force-field and Gromacs version, those parameters are 
listed in:

Not withstanding, don't forget reading the manual!


Dr. Mauricio P. Sica                    LEPP
Phone: (54011)4365-7100 ext. 169        Laboratorio de Expresión
R. Saenz Peña 354                       y Plegado Proteico
(B1876BXF) Bernal, Buenos Aires         Universidad de Quilmes

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