i am running dynamics on Protein-RNA complex using Gromos 96 43a1 force field. While using grompp command, i came across the error which stated that the number of coordinates in solv.gro does not match with that in the topol file. I have tried using all the ways to correct this error using the answers i read, but still i am not able to do it. i have tried deleting the SOL molecules from topol file also. kindly let me know how the protocol varies for protein-RNA complex.
GROMOS is a poor choice for a simulation including RNA. Use a better force field like CHARMM or AMBER. In fact, I'm not sure how you got a topology, as trying to build a nucleic acid topology with pdb2gmx and GROMOS usually fails.
As for the protocol, there's nothing special. It's like any solute-in-water simulation.
If You have a single trna molecule without adduct like aminoacyl on the end or any modification of residues - selectino of amber99 series of force fields will be enough to generate topology with gromacs... in addition, last PO2 group on 5'-end of trna molecule should be croped and then both, 5' and 3'-ends, will be automatically capped with hydrogens. Its an approximated model of charge assignment, which is neccessary to avoid sharp changes in charge distribution along the molecule and stabilze structure during MD..
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