AMBER: rmsd calculation in ptraj II

From: gurpreet singh <>
Date: Sat, 10 Mar 2007 20:37:10 -0800

hello amber users

i m using ptraj module of amber9 to calculate the rmsd( backbone only) over
the whole trajectory of the simulation taking the crystal structure as the
reference and i m getting values in the range of 35 to 38 although there is
no significant change in the structure during the simulation. To verify
the results i calculated the rmsd of the individual structure using VMD and
their the rmsd is coming fine as expected.

the command which i used in ptraj was:
strip :WAT
reference my crystal structure.pdb
rms reference out rmsbackbone.dat :1-339.CA

if the problem is in the input then please tell me the suitable corrections
i need to make and if not suggest some other ways by which i can rectify
the problem


Gurpreet Singh

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Received on Sun Mar 11 2007 - 06:07:42 PDT
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