Dear Dr. Mauricio P. Sica, Thank you for your reply! Can you give me an detailed example?
ÔÚÄúµÄÀ´ÐÅÖÐÔø¾Ìáµ½: >From: "Mauricio Pablo Sica" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users <[EMAIL PROTECTED]> >To: [EMAIL PROTECTED] >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: > >$GMX/gromacs/top/ff*bon.itp > >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 >Argentina >________________________________________________________________ > > > > >_______________________________________________ >gmx-users mailing list [EMAIL PROTECTED] >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/search before posting! >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to [EMAIL PROTECTED] >Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
