Strictly speaking, you do not *need* a .gro file. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. If you prefer .gro format and have a .pdb file, just use editconf to transform between formats.

For dealing with ligands, complex topologies, and merging coordinate files, etc. please see my tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html.

Just use ATB to start, rather than trying to hack a PRODRG topology. ATB is much more reliable, in my experience.

Dear Mr. hanoun,

Using quantum charge calculation (eg. resp charges in Gaussian 09) is the best way to assign partial charges of ligands. As you mentioned, Use PRODRG or ATB to create your topology file then change partial charge with quantum results.

Hope it helps,

HHA

I can't obtain .gro file from ATP so I need to use this method ,

and about Q charge calculation , the Gaussian 09 is not freely available .

if there are any other reliable one , please tell me about it .

Dear Mr. hanoun,

R.E.D is a free software which automatically calculates RESP and ESP charge values

download link :

http://q4md-forcefieldtools.org/RED/

best,

HHA

A few things:

1. There is no need for a .gro file at all. Gromacs can deal with whatever coordinate format you prefer, so if you have .pdb, for instance, that's perfectly fine.

2. Be careful with QM calculations - there are no published methods for how the Gromos people did their original calculations, so it's not straightforward to do the charge calculations. I contacted their developers many years ago and was told that they did some "simple DFT calculations" and then fit charges to the electron densities empirically. So, in reality, there is likely to be almost no connection at all to QM-calculated charges. We tried to determine a few potentially useful methods in http://pubs.acs.org/doi/abs/10.1021/ci100335w, just be advised that Gromos parametrization is VERY empirical.

Dear Mr. Stéphane ,

I mean ATB server not ATP molecule

sorry for interuption

Dear Mr. Justin,

I need .gro file to proceed the simulation steps .

As I know ,gromacs produce .gro file from pdb file by pdb2gmx but it gives error with the ligands as they not defined in itp file of the forcefeild , so I parameterize it with PRODRG or ATB . PRODRG produce .gro file that it's coordinate taken and merged with that produce by GROMACS .......How can I merge different coordinate in one file ?? (they have different position)

Strictly speaking, you do not *need* a .gro file. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. If you prefer .gro format and have a .pdb file, just use editconf to transform between formats.

For dealing with ligands, complex topologies, and merging coordinate files, etc. please see my tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html.

indeed , I use ur tutorial to make my simulation .

my problem was solved by using editconf , but I had a new problem that the atoms' name and arrangement of my pdb file not match that names and arrangement of itp file obtained from ATB .