Hi - I would like to run MD simulations on mutated proteins (misense SNPs in particular). I have used a fasta format file with the misense mutation embedded in the sequence as input to I-TASSER. I-TASSER has in turn produces 5 models that I can choose to send to GROMACS. I have used
gmx pdb2gmx -f mymodel.pdb -o mymodel.gro
to get my mutation pdb file into .gro format.
I am currently a bit stuck as to how I then take this new .gro file and perform md simulation using GROMACS. I understand I can use
gmx mdrun <options>
however there doesn't seem to be an option use my .gro file as input to mdrun. I suspect I am missing some intermediate steps.
Could someone point my in the right direction? Thanks very much.