Another way is "Write current/Write complex" from Autodock PLAY mode widget. Save the complex in ".pdb" format.

Open complex in PdbEditor (http://pdbeditor.sourceforge.net) --> Save it again.

Other than above said, if you just want to convert your .pdb file to .gro then, use this command

gmx editconf -f complex.pdb -o complex.gro

Hey,

First convert the docked complex to a PDB file. Link: http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-protein-ligand-complex-as-a-pdb-file-in-autodock

Then generate topology for the complex (both protein and ligand) as described here :

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html

Another way is "Write current/Write complex" from Autodock PLAY mode widget. Save the complex in ".pdb" format.

Open complex in PdbEditor (http://pdbeditor.sourceforge.net) --> Save it again.

Other than above said, if you just want to convert your .pdb file to .gro then, use this command

gmx editconf -f complex.pdb -o complex.gro

Thanks syed for your reply, i tried teh same way but on obtaining complex.pdb (for receptor+docked ligands' poses), then on converting pdb to .gro file , the system is saying that ligand entry not found in residue topology database.

thankyou pragna for the valuable info, it worked . now have to check for my system.

Hi Syed,

when i executed this command while obtaining complex.pdb file from AUTODOCK , Its showing me error.

set a=`grep ENDMDL my_docking.pdb | wc -l` set b=`expr $a - 2` csplit -k -s -n 3 -f my_docking. mydocking.pdb '/^ENDMDL/+1' '{'$b'}' foreach f ( mydocking.[0-9][0-9][0-9] ) mv $f $f.pdb end

Hi Shivani,

You are encountering "ligand entry not found in residue topology database" fatal error because the force fields available in GROMACS do not recognize your ligand http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database . You need to generate topologies for ligands externally using servers such as ATB compbio.biosci.uq.edu.au/atb/ (used for GROMOS96 ff).

To achieve this, first you need to separate the coordinates of protein and ligand i.e, in a separate PDB file. Then generate the topology and .gro for the protein using PBD2GMX. For the ligand, you need an external server to generate the topology and .gro file. Finally, you need to merge the .gro files of both protein and ligand and edit the topology file as well.

The detailed description about the whole process is explained here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html

thanks syed, trying this way only.. Thankyou fr ur help