Dan or others might have better answer but if you like Python, you can
try pytraj (wrapper of cpptraj).
This is an example script to calculate rmsd between two different proteins.
https://gist.github.com/hainm/465819f51a48ac042e3a
pytraj: https://github.com/pytraj/pytraj (still in beta version though)
Hai
On Thu, Feb 19, 2015 at 1:09 PM, Nicole Ippolito
<ippolito.nicole89.gmail.com> wrote:
> Hello,
>
> I am trying to calculate the RMSD between an Apo structure and a structure
> with the substrate bound. Is there a way to do this through cpptraj?
> Currently, I am attempting the following command.
>
> parm parm0
> parm parm1
> trajin
> /home/aubndi/Monoxygenase/Apo/Analysis/Cluster/Apo_mon_aMD_avg_0_1000ns.crd.gz
> parmindex 0
> trajin
> /home/aubndi/Monoxygenase/FMP_OCS/Analysis/Cluster/FMP_OCS_mon_aMD_avg_0_1000ns.crd.gz
> parmindex 1
> reference Apo_mon_aMD_avg_0_1000ns.crd.gz parmindex 0
> rms first out FMP_OCS_mon_RMSD_aPO.out time 0.005 :1-363
>
> It is telling me that the prmtop files do not match; however, they worked
> fine when just doing the RMSD for the individual proteins. I am assuming it
> is something I am doing with my commands. If you have any advice that
> would be great.
>
> Thank you,
> Nicole Ippolito
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Received on Thu Feb 19 2015 - 12:00:02 PST
