Hi [email protected], I think it's better to only use PRODRG for the pyridoxal phosphate part. Then you can process the rest of the protein as usual, preserving the parameters for lysine backbone and side chain. The PLP part you can renumber and merge with the protein topology, adding bond, angles and dihedrals for the connection. Alternatively you could rewrite the PLP topology as a .rtp entry and add the connection in the file specbond.dat.
Hope it helps, Tsjerk On Fri, Jul 3, 2009 at 9:03 AM, hazizian<[email protected]> wrote: > Hi > I want to do MD with a protien with prydoxal phosphate(PLP) which attache > covalently to one lysine. > For this I extract the Toplogy of lysine-PLP from PRODRG server.(DRGGMX.ITP > and DRGPOH.PDB).I Changed the name DRGGMX.ITP to DRG.itp. > after donig > pdb2gmx -f m.pdb -o m1.pdb -water spce with the protein without PLP > (m.pdb=protein whitout covalent bond) , I modified the topol.top file > followig this: > 1- add "DRG.itp" under the forcefield section on topol.top > 2- add "DRG 1" under the molecule sectin of topol.top > also I modifed m1.pdb: > cut the related lysine (LYS 360) in the m1.pdb and paste the modified lysine- > PLP (DRG 360)coordination from DRGPH.PDB. > then I do editconf -f m1.pdb and genbox -f m1.pdb successfully, but when I > want to do grompp the following fatal error appeared: > There is no DRG moleculetype. > what should I do now? > Thanks. > -- > Tehran University of Medical Sciences > www.tums.ac.ir > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] http://lists.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
