Dear Amber users,
I am trying to do RMSD calculation after different fitting approach using
a single cpptarj input file. I am trying to accomplish this in the
following way. The cpptraj.in file contains,
***************************************************************************************
trajin ../4md.crd
autoimage
reference ../start.crd
rms reference out RMSD.dat time 2 :1-604.CA,N,C,O
rms reference out RMSD_mainloop.dat time 2 /
:10-40,52-74,86-223,237-287,302-318,352-372,387-485,504-528,546-600.CA,N,C,O
rms reference out RMSD_allLoop.dat time 2
:10-20,25-30,34-40,52-61,66-74,86-125,130-139,147-152,157-165,174-175,180-186,193-199,/
207-211,217-223,239-244,249-255,260-265,282-286,303-307,313-318,353-358,368-371,389-392,397-405,415-421,430-434,437-461,467-484,504-512,515-524,547-564,568-585.CA
,N,C,O
*****************************************************************************************************************
and I run it by 'cpptraj file.top < cpptraj.in
Am I doing anything wrong here?. I have seen from the tutorials that the
'rms' command modify the confidantes and effect all the subsequent
commands. Do I need to do these three different RMSD calculation separately?
Thanks in advance
Anu
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Received on Fri Oct 16 2015 - 05:30:04 PDT
