sounds like you have an imaging problem- this is easily fixed. search
the archives for ptraj and image.
On Mon, Apr 4, 2011 at 10:00 AM, Sarah Eliabeth Rowe <bb8860.wayne.edu> wrote:
> 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 - 07:30:05 PDT
