Hi Sana,

you can use I-mutant for investigating the effect of NS mutations on protein structure instead of Discovery studio.

I-MUTANT available on:

http://folding.biofold.org/i-mutant/i-mutant2.0.html

Dear Sana,

INPS is another tool (https://www.ncbi.nlm.nih.gov/pubmed/25957347) for predicting the impact of non-synonymous variations on protein stability from sequence (http://inps.biocomp.unibo.it).

Thanks,

Amin

I'm not familiar with Discovery Studio, but Charmm-gui makes running MD simulations of SNPs very easy via their web-interface that generates all the files necessary to run MD for most common packages.

Check it out at: http://charmm-gui.org/?doc=input/mdsetup

You can generate models of your mutant protein using any sequence manipulation tool or modelling tools then run simulations on Gromacs.