Hi,
On Thu, Feb 19, 2015 at 11:09 AM, Nicole Ippolito <
ippolito.nicole89.gmail.com> wrote:
> 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
>
It would be better here if you posted the exact error message. The key with
the RMSD calculation is the number of atoms and the atom ordering must
match between the reference and target structures. So if both your target
and reference have the exact same residues between 1 and 363 this should
work. Can you either paste or attach your complete cpptraj output so I can
take a look? Thanks
-Dan
PS - You may be interested in the RMSD-related cpptraj tutorial here:
http://ambermd.org/tutorials/analysis/tutorial1/
> 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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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Feb 19 2015 - 12:30:02 PST
