Hi everybody,
I'm measuring the backbone RMSD of a 2ns equilibration trajectory against the crystal structure.
Using the VMD RMSD trajectory tool and having as reference the crystal structure I obtained the following results:
id mol avg sd min max num
0 2wc6.pdb 0.000 0.000 0.000 0.000 0
1 2wch_bal_solv.prmtop 1.222 0.084 0.987 1.481 1000
Using the following ptraj input file:
trajin equil_2ns.mdcrd.gz 1 1000 1
reference 2wc6.pdb
rms reference out equil_0-2ns.rmsd .CA,C,N
I obtain the results shown in the attached snapshot. 15+ Angstrom?
Any suggestions as to the observed discrepancy would be greatly appreciated.
Best regards
George
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Received on Wed Jan 04 2012 - 10:30:02 PST
