Gromacs And Modified Residue

Question

[Raygozak]

Hi, i'm trying to run an MD simulation of a protein with a tRNA and i'm getting an error that it does not recognize the modified residue H2U (DHU), i tried changing the forcefield to one that was user contributed but didn't work either. can anyone point me to some resource or tell he how you solved it? i've already googled it without success

thanks

Answer 1

[Pappu]

The residue name must match to the name given in the rtp file of the forcefield. Check the forcefield directory and rename your atom. gromacs-users mailing list already contains answers to such questions.

Answer 2

[João Rodrigues]

What you want to look at is called "parameterization". It's a tough job.. I'd look into ATB to see if there is something like your residue in there. Otherwise, you can use PRODRG to build a topology for the residue on your own. Have a look at this paper and this webpage for more details.