[gmx-users] protein covalently bond to ligand

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jul 3 12:03:48 CEST 2009

Hi hazizian at razi.tums.ac.ir,

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,


On Fri, Jul 3, 2009 at 9:03 AM, hazizian<hazizian at razi.tums.ac.ir> 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    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> 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

More information about the gromacs.org_gmx-users mailing list