I used ptraj with the following input file:
trajin g1tetra_prod_mdx1
trajin g1tetra_prod_mdx2
rms first out g1tetra_rms_1_112.dat :1-112 .CA, C, N
strip :WAT
go
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wed, March 23, 2011 6:15:58 PM
Subject: Re: [AMBER] odd output from rms measurement
We need to know how this was calculated.
On Mar 23, 2011 5:56 PM, "Chris Chris" <alpharecept.yahoo.com> wrote:
Can someone help me explain the attached graph? Basically, I'm simulating
binding energies of a group of artificial peptides. I replaced the side
chains
of tropomyosin with the side chains of my peptides. I'm doing long
production
simulations so that the structure can 'acclimate' to my grafting of the new
side
chains
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Received on Wed Mar 23 2011 - 17:00:03 PDT
