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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 19 2015 - 10:30:02 PST
