using gromacs to run molecular dynamic simulation of SNP
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6.9 years ago
arronslacey ▴ 310

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.

gromacs molecular-dynamics SNP md • 2.1k views