Create them from what?  You can write converters to transform force fields from one format to another (e.g. CHARMM to GROMACS, AMBER to GROMACS, etc) but that requires preexisting information. If you've got some custom force field you want to implement, a new residue, etc. the only way to create these new force field files is to fire up your favorite text editor and begin creating them. The file formats are very straightforward and described in the GROMACS manual.

Dear Justin

Thanks, to explain a little more about my question regarding your answer, We have a glycoprotein that is glycosylated in ASN361. First, glycosylated asparagine was extracted as a new residue from pdb file and then topology files were generated by Swissparam. Now how to convert the style of topology files to proper format for adding to the related files (.rtp, .itp, .hdp .atp and .dat) in gromacs force fields? Please find attachment.

Thanks

Hesen Aryapour

If you have a glycosylated Asn, you shouldn't be doing anything to Gly.

There is only one way to approach this - open up the existing .rtp file in a text editor, copy the ASN entry, rename it, and modify it according to whatever parameters you need to use. Note that CHARMM supports glycosylated amino acids, so using SwissParam is not necessary; highly optimized parameters already exist. You'll still have to do the same work to create a new .rtp entry, but you should be sourcing the parameters from the CHARMM files themselves (see our group's webpage), not SwissParam. Combining generalized parameters with optimized protein parameters is not the proper approach. Servers like SwissParam and CGenFF/ParamChem should be used for standalone molecules or initial guesses for new residue parameters only.

Thanks for everything

I used "Glycan Reader" at CHARMM-GUI to read carbohydrate structures from a PDB file into CHARMM and the calculated results is included to this comment. Can I use from cgenff_charmm2gmx.py to convert the results to gromacs format? this way is true?

The converter script is designed to work on a single residue (standalone ligand) so no, it is not applicable here. You can get all the information you need for building an .rtp entry from the PSF itself, or see if the normal CHARMM-GUI Input Generator will build the system. It writes complete GROMACS topologies and inputs.

Justin Lemkul : Hello Justin,

I have a system having (clays + ions + small organic molecules), which I created in Material studio.

This is what I did: For organics, I am using CHARMM36 forcefield. After having the following files ~ (.mol2 and .str) from Zinc15 and CGenFF, I later used cgenff_charmm2gmx.py to get 3 files (.itp, .prm, .top). So far so good. Now for the clay system, I exported the (.pdb) structure from Material studio. Here I face a problem,since I am using ClayFF (clay force field) for my clays, can you suggest me how to create an ( .rtp) file for ClayFF suitable for GROMACS?

I already have these files in my Clayff directory : (spce.itp, ffbonded.itp, ffnonbonded.itp, forcefield.itp, ions.itp and atomtypes.atp ).

Thanks a lot!

Deb

You can go through GROMACS tutorials http://www.mdtutorials.com/gmx/

I hope there you would get your required information.

I have a DNA file but it is broken and it should be...so can any one do this for topology. i want to use Amber99sb. i am attching here.

Thank you