> Iam preparing my protein for molecular dynamics simulations. In my
> first step I used tleap to get the parameter and topology files
> and the new pdb structure which I made from these files using
> ambpdb command has completely different coordinates than the
> original pdb structure.
> The same happened with minimization using Sander. The resulting
> minimized strucure has completely different coordinates than the
> one I used before minimization. Are these issuea bugs in the
> program or am I doing something wrong.
This is normal, You can RMS-fit to your original crds in ptraj
if you want them similar.
Bill
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Received on Thu Jul 29 2010 - 12:00:36 PDT
