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.
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