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

[Bratin Kumar Das]

Use the .tpr file generated by grompp module

On Wed 8 Jan, 2020, 9:43 PM Matthew Fisher, <matthew.fisher at stcatz.ox.ac.uk>
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.
>
> Best wishes,
> Matthew
>
>
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