[gmx-users] Re: script to constraint distance between ligand and protein

David Mobley dmobley at gmail.com
Thu Mar 18 14:41:27 CET 2010


I don't have a version of this tool that I'm comfortable distributing at this point (for what it's worth, the message you're referring to is almost 4 years old!). 

You should be able to get help with your specific topology file problem on-list. 

Free energy calculations are one of the hardest things you can do with gromacs. I'd encourage you to start by doing some plain simulations in gromacs before trying to set up free energy calculations.

The specific error you are seeing is undoubtedly because the protein in your system only contains 2591 atoms and you are trying to add restraints between some atom in the protein and atom 2606, which you think is in the ligand. For restraints to work, you need the protein and ligand to be part of the same [ atoms ] section in the topology file, so that the ligand will be numbered consecutively with the protein. (Technically, the protein and ligand must be part of the same gromacs "molecule", even though they are not connected).

Again, this should go on-list. 

On Mar 18, 2010, at 7:48 AM, sunita gupta wrote:

> Hi David
> I appologise for bothering on your personal mail id again as you have already told me not to interrupt u personally.....
> bt after going through the mailing archive http://www.mail-archive.com/gmx-users@gromacs.org/msg03610.html, you have suggested use of a script which can be asked off-list.
> I am really new to gromacs and trying to calculate binding free energy of a protein-ligand.. After referring through many research articles...I got to know to add restraints on the bond, angle and dihedrals of protein and ligand, as it is also involved in thermodynamics cycle.
> I tried to add distance restraints between a protein and ligand atom and encountered with the following error
> Fatal error:
> [ file 3z.top, line 16103 ]:
> Atom index (2606) in distance_restraints out of bounds (1-2591).
> Kindly send me that script which can merge the topologies for ligand and protein, I have individual .top and .gro files for protein and ligand.
> Thanks in Advance
> -- 
> Best Regards

David Mobley
dmobley at gmail.com

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