Dear amber,
I wonder what should I do to calculate RMSD and RMSF with the ptraj module
in AMBER.
1.My input file for calculating RMSD is as following £º
trajin last20ns.mdcrd
reference protein-wat.inpcrd
rms reference out rmsd.dat :1-229 time 0.2
There I¡¯d love to know whether my input file is right ?
I also want to know whether my calculation value was calculated by taking
the RMSD of initial structure as reference?
2.My input file for calculating RMSF is as following :
trajin last20ns.mdcrd
rms first out a.rmsd :
1-229.CA,C,N time 0.2
atomicfluct out protein-backbone.dat :
1-229.CA,C,N
I want to ask the following two questions :
i. The meaning of the first is the first snapshot in the trajectory or the
initial structure ?
ii. If I use the average structure as recommended by the manual of Amber
,should I change first to average in my input file ?
My new input file is as following : trajin last20ns.mdcrd
reference ave.pdb
rms reference out a.rmsd :
1-229.CA,C,N time 0.2
atomicfluct out protein-backbone.rmsf :
1-229.CA,C,N
I want to confirm the above input file is appropriate or not .
The method for calculating ave.pdb is as following :
trajin last20ns.mdcrd
average ave.pdb pdb
We are looking forward to your replay .Thank you much for your kindhearted
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 30 2012 - 01:00:03 PDT
