[gmx-users] RDF calculation from surface of protein

[Pandya, Akash]

Hi all,

I am trying to calculate the RDF between the protein surface and the centre of mass of my ligand and water molecules. Please find below the command I used:

gmx rdf -s proteinLIG.tpr -f proteinLIG.xtc -n index.ndx -o rdf.xvg -bin 0.02 -cn number.xvg -surf mol -seltype mol_com


I get the following error:



Inconsistency in user input:
-surf only works with -ref that consists of atoms

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I am wondering what this error means? My ref group does contain atoms? Any guidance will be much appreciated :)


Akash