Dear researcher,
I am working on molecular dynamics simulation. I did the MDS of protein ligand complex. Currently i am working on urea induced denaturation of proteins.
I have generated urea topology files from prodrg server but when i want to neutralized that system it showed much more charges which is not possible. I concluded that my topology files have errors.
Please provide me urea.gro and urea.itp file for Gromos 9653a6 force fields or any other force fields.
You can use your urea.gro file as it doesnt contain partial charge definitions.
I found urea with a google search (for the amber force field). The partial charges sum up to zero:
https://github.com/gromacs/gromacs/blob/master/share/top/amber03.ff/urea.itp
If this still doesnt work you can calculate the partial charges yourself using the RED server:
http://upjv.q4md-forcefieldtools.org/REDServer/
regards,
Martin
Urea is present in every force field provided in GROMACS. Just use pdb2gmx.
Justin sir,
I took a pdb file of urea and then tried to convert in to .gro file but it is showed a error that UNK is not defined in residue topology database
Look in the .rtp file - surely you will confirm there is no such thing as "UNK," which is a default name (unknown) that many programs assign to residues. You will, however, find "UREA" in the .rtp file, so adjust your input coordinate file so that the residue and atom names match what the force field requires. pdb2gmx is not magic!
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