AMBER Archive (2009)

Subject: [AMBER] ptraj image

From: Neha Bharat Gajaria (
Date: Wed Dec 09 2009 - 00:13:36 CST

Hi List,

I have a system which has two antiparallel monomers. I m using the following
commands below using Amber 9. I can get the correct distances between Ca-Ca
but the values get messed up with helix.rmsd and equil.rmsd after 90 ns. Any

trajin prod197.mdcrd.gz 1 50 1
trajin prod198.mdcrd.gz 1 50 1
trajin prod199.mdcrd.gz 1 50 1
trajin prod200.mdcrd.gz 1 50 1
trajin prod201.mdcrd.gz 1 50 1

center :1-144 origin mass
image origin center

distance CALPHA :62_at_CA :137_at_CA out dist_CALPHA.list
distance HIPGLN :7_at_H :32_at_NE2 out dist_HIPGLN.list

reference pro_solvated.inpcrd

rms reference out equil.rmsd @CA,C,N
rms reference out helix.rmsd :54-71_at_N,CA,C,:126-143_at_N,CA,C
rms reference out helix1.rmsd :54-71_at_N,CA,C
rms reference out helix2.rmsd :126-143_at_N,CA,C

Many thanks,

Neha Gandhi Gajaria,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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