Hi,

if you want to run a Molecular Dynamic with gromacs you need to use pdb2gmx command, but if you need the .gro file you can use the gromacs command: editconf -f file_in.pdb -o file_out.gro

Dear Wan,

editconf command doesn't convert the .pdb to .gro but rather it defines the box or manipulates the coordinates generated before which is to be used to generate the box. Before using editconf command, you have to generate the topology in gromacs format (.gro) from .pdb by using pdb2gmx command and then you run editconf. I hope this helps.

Regards,

I usually hate it when people forward a link, but this particular link was tremendously helpful to me.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/

This tutorial helps with everything needed to set up a standard protein for a GROMACS MD simulation as well as provides some direction for analysis.

I think,

It may be possible using Open Bable software for converting .pdb file to GROMACS MD simulation.

http://openbabel.org/docs/2.3.0/FileFormats/Overview.html

There will be an option for converting .pdb to .gr96. Gromacs coming under the Molecular dynamics and docking formats (Supported file formats).

use pdb2gmx command.

Hi,

if you want to run a Molecular Dynamic with gromacs you need to use pdb2gmx command, but if you need the .gro file you can use the gromacs command: editconf -f file_in.pdb -o file_out.gro

Hi, 

My concern is to convert hetero atom coordinate file from pdb to gro.

i have even tried with openbabel, but it gives different results as compared to prodrg server that i used. so dont knw which one is better.

can any1 help me :(

Hope I'm not late, I believe that you want to introduce an "exotic" (not included in the force field default database) molecule. In this case the procedure gets a little more complex, e-mail me if you want more info on how to approach this. In any case as stated before in order to convert a .pdb to .gro all you have to do is run pdb2gmx select your force field, solvent and you are done.

you can easily convert pdb and gro files to eachother with USCF chimera and VMD softwares. inspite of these, if you are working eith gromacs use this command:

editconf .pdb to .gro

How to convert the .gro file to pdb in VMD as i need the final structure in pdb format and something went wrong with my gromacs path.Kindly do help me

Hi Devo kanta Pegu, hope you I'm not late to answer your question. To convert .gro to .pdb in VMD, you need to load the .gro file into VMD. Select the entry in the VMD Main window and go to File menu. Select Save coordinates. You can select file type as .pdb and "all" in Selected atoms drop menu. Finally save the output at desired location with desired name.