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

[Justin Lemkul]

On 1/8/20 11:12 AM, Matthew Fisher wrote:
> 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.

The latter is the best approach as it will allow for proper 
mass-weighting in the RMSD calculation.

-Justin

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Justin A. Lemkul, Ph.D.
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