Calyff in Gromacs

User discussions
#1

Brief description of tools/files:
Hi,
Iam new in Gromacs and

I am trying to use Clay.ff with Gromacs.

I added Clayff.ff directory in my working directory (downloaded from the link below:
https://github.com/thomasunderwood/ClayFF )

and I run the command:

gmx pdb2gmx -f xxx.pdb -o xxx.gro

I got the error message:

“Could not find any files ending on ‘.rtp’ in the force field directory”

Indeed the Clayff.ff directory did not have an rtp file.

What should I do?

Link:
Contact person (name and email address):
George Papamokos
george.papamokos@gmail.com

How the work has been tested/reviewed:

#2

Hi,

I had a brief look at the files you link and this seems to be very initial work from “thomasunderwood” of porting the clay force-field to gromacs.

Trying to contact the author directly might help.

#3

Here is a link to a publication where people used clayff and gromacs, they might be able to help you out: https://www.tandfonline.com/doi/full/10.1080/08927022.2010.513008

#4

I would echo the suggestion to contact the author, who has posted a tutorial but it lacks a lot of detail, starting from a pre-constructed topology. Note that this force field and its intended use is very different from “normal” GROMACS workflows and you cannot use pdb2gmx for it. Rather, topologies of surfaces and materials should be generated with x2top, which allows for the processing of generic species based solely on distances between the atoms.

#5

Hi,

I know I’m late to comment, but I use Clayff and Interface FF in Gromacs a lot. Let me know if you want any help…

Michael Holmboe
Umeå university, Sweden