[gmx-users] does gromac "mdrun" produce predicted 3d structure?

[Arron Lacey]

Hi everyone - I have used I-TASSER to generate pdb files for missense 
SNPs. I understand there are some reservations about the accuracy of SNP 
structural changes by using homology based methods alone. Can GROMACS 
off anything better? I have used

gmx mdrun <options>

to calculate the energy minimization of the pdb files that I-TASSER 
outputs, but I want to know if mdrun can produce the predicted 
co-ordinates of the structure due to the SNP (if there is any change 
that is)?

Also - does there a better way to embed a SNP in a wild-type pdb file 
for input to pdb2gmx?

Thanks very much.