AMBER: constraint pdb file

From: Stern, Julie <>
Date: Mon, 5 Mar 2007 16:06:47 -0500

     I'm trying to restrain a molecule putting a force constant in column O of my pdb.
However, it seems that the original pdb file coordinates, the prmtop+inpcrd file coordinates,
and the coordinates coming from leap using savePdb are all different. I was then able
to use ambpdb with the prmtop + inpcrd files to create a pdb aligned with the prmtop + incprd.
So, I now have the proper reference file. When I sent to add the force constants to column
O, I discovered there was no column O or column B.
      Can anyone tell me how I may generate a column O using ambpdb or any other way?
I don't know how vi can do it for example. I'm sure I can do an alignment in vmd and
save the coordinates from the orignal pdb file, but I was concerned with roundoff.
But is there a ambpdb way to do this?
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Received on Wed Mar 07 2007 - 06:07:28 PST
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