[AMBER] rmsd rmsf

From: Yanyan MENG <mengyanyan21.gmail.com>
Date: Tue, 30 Oct 2012 15:50:10 +0800

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

trajin last20ns.mdcrd

reference protein-wat.inpcrd

rms reference out rmsd.dat :1-229 time 0.2

There Id 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
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Received on Tue Oct 30 2012 - 01:00:03 PDT
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