Hi everyone,
I am trying to use ptraj to calculate the rmsd of the backbone of a protein after heating compared to the initial structure. The protein was heated from 0 to 300 over 5 ns. When I go to calculate the rmsd it is fine (around 1 or so) until step 2965 when it suddenly jumps to 50. The protein that I am looking at has two structures, which were heated separately, but when checking the rmsd both jump to 50 at the same step. I have graphed all the energies and the temperature and there are no large jumps, and when looking at the structure in vmd there doesn't appear to be any large/significant conformational change.
The strange thing is that if I make a pdb from the restart file using ambpdb and check the rmsd it is fine, but if I make a pdb from the last frame of the mdcrd file using ptraj I get a completely different pdb from the one made with ambpdb. Has anyone ever experienced this before, or have any ideas as to what is going wrong?
Thanks,
Sarah
This is my input for ptraj to calculate rmsd
trajin COMPLEX_HIS_OUT.xleap.pdb
trajin 1.mdcrd
rms first out rms_002.out :1-56.CA,C,N,:64-149.CA,C,N,:159-250.CA,C,N
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Received on Mon Apr 04 2011 - 07:30:03 PDT
