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

Rui Li moonfine at mail.sdu.edu.cn
Fri Apr 13 16:03:38 CEST 2007

Dear Dr. Mauricio P. Sica,

Thank you for your reply!
Can you give me an detailed example?

>From: "Mauricio Pablo Sica" <msica at unq.edu.ar>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] Re: simulate a substrate-bound enzyme
>Date:Fri, 13 Apr 2007 09:10:24 -0300
>> 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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