We did whole exome sequencing and found some candidate SNVs for our genes of interest. Results of queries from precomputed results of prediction programs gave some idea about the variants. For example, one variant may have prediction results as following
SIFT: 0
PolyPhen2: 1
MutationTaster: 0.99
MutationAssessor: 4.81
FATHMM: -3.84
GERP++ RS: 5.8
PhyloP: 2.76
They are all useful to prioritize and filter the variants. But with some variants I want to have deeper look at them, like doing molecular dynamics simulation of the variants. From what I found, GROMACS seems to be an appropriate tool. I have installed GROMACS with GPU support. However, reading many documentations and references is too much to get started. Therefore I cookbook guide for this specific case will be very nice.
I am also open for suggestions of using other tools or different approaches.
__Update 1__: It worth to note that I do not have PDB files for some proteins.
