[gmx-users] Comparing the RMSD of an in silico variant to a crystal structure.

[Matthew Fisher]

Dear all,

I'm simulating the effect of amino acid mutations on tertiary structure and, for benchmarking purposes, I want to compare the RMS of my in silico variant trajectories (prepared from the WT structure) to their cystallographic structures.

In the gmx rms command, when I select the structure for the -s flag, should I use the pdb file from the RCSB, or alternatively should I take the crystal structure, parametise it using pdb2gmx and then take the pre-minimisation .tpr file? Alternatively is there something else I should be doing? Any advice would be appreciated.

Best wishes,
Matthew