The easier way I've been able to achieve this is by using loadcrd and crdaction commands, ie:
loadcrd md1.traj
crdaction md1.trj rms first :{mask}
crdaction md1.trj average avg.trj
So from what I understand this will load your trajectory as a coordinate data set, the rms command overwrites this file in memory (not the file on disk!) to rms fit each frame to the first frame as a reference, using whatever mask you provide (:* fits all residues), and then average averages the trajectory to get a single frame with average trajectory and saves it to avg.trj. You can then use trajin with your original md1 file to do the rms with your average as a reference.
Be careful if you have waters in your trajectory/parm, as sometimes that will mess up the rms fit. You can use strip to get waters out if the average structure looks funky in VMD.
Matt Alegrete
California State University, Northridge
> On Sep 17, 2014, at 7:17 AM, newamber list <newamberlist.gmail.com> wrote:
>
> Hi All
>
> I have seen papers and they report rmsd plot using average structure as a
> reference but they dont mention how did they obtain average structure? I
> also want to plot rmsd with average structure as reference.
>
> In amber archive it has been suggested to do first RMSD fitting then
> calculate average structure over msd fitted. Like this:
>
> trajin md1.trj
> rms first out rms.dat :1-100
> average avg.pdb pdb
>
> But which structure to be chosen as 'first' (let it be from some
> equilibrated part?) or just I should use average without RMSD step:
>
> trajin md1.trj
> average avg.pdb pdb
>
>
> Also as I googled some people use RMSF to get average strcutre.
>
> I am not sure which is best/better way of considering average structure
> (RMSF or RMSD)
>
> Thanks for any suggestions
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Received on Wed Sep 17 2014 - 09:30:03 PDT
