Nicole,
My guess is that it isn't your commands per se, but that your prmtops don't
match because one of them is just protein, and the other has the substrate
present. That means there's a different number of atoms present, so it's
causing to spit the error out. I think if you stripped out the substrate
with parmstrip, you should be able to run it, but I'm assuming here you're
interested in the protein movements and not the substrate itself.
So the new input would be-
parm parm0
> parm parm1
>
parmstrip :SubstrateName
And that should solve your problem. assuming there's no other weird atom
mismatches.
That said, it also depends on what you're trying to compare. If you're
trying to compare trajectories of your apo and substrate system relative to
their respective starting frames/reference structures (which I think is the
case here), then you can also try something like this-
trajin substrate.mdcrd
reference apo.pdb
rms reference out rms .CA
Where you'd have to make sure that the substrate isn't in the
substrate.pdb, or specify what residues you want to align, and vice versa.
If you wanted to get apo's trajectory in reference to substrate, then you'd
just change the reference to substrate.pdb and the apo trajectory.
If you are in a situation where you do want to keep your substrate as part
of your RMSD calculations, what I'd do is align the trajectories to their
starting position separately, then just feed the outputs into a plotting
program, ie Excel, grace, to compare them.
Best,
Kenneth
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 - 11:30:02 PST
