AMBER Archive (2007)

Subject: AMBER: rmsd calculation in ptraj

From: gurpreet singh (gps.iitm_at_gmail.com)
Date: Sat Mar 10 2007 - 07:38:28 CST

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 :mask

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

thanks

Gurpreet Singh
MS
DEPT OF BIOTECHNOLOGY
IIT MADRAS
INDIA

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