AMBER Archive (2008)

Subject: AMBER:

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Thu Mar 06 2008 - 12:04:01 CST

Hi Amber

I am trying to obtain an rms from separate regions of my protein. That
is I want to leave out a center fragment of the protein for my analysis.
I have tried the following and derivations of the following, but have
been unsuccessful.

 

 

Trajin file.mdcrd

Reference fileref.pdb

Rms reference out file.txt time 5 :1-200_at_C,N,O :300-400_at_C,N,O

 

Go

 

Notice I am trying to get rms leaving the peptide sequence of 201-299.

 

Is this possible with ptraj?

 

Steve

 

 

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