[gmx-users] RDF calculation from surface of protein

[ISHRAT JAHAN]

-surf flag is used with -ref flag. Provide the reference file in the -ref
flag.

On Thu, Feb 6, 2020 at 1:52 AM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
wrote:

> 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
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-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh