[AMBER] CHAMBER and making PDB files

From: Seibold, Stephen <Seibold79.stmary.edu>
Date: Wed, 1 Jun 2011 17:34:55 +0000

Hello
I used CHAMBER to create a AMBER topology file and input coordinates. I then obtained, doing MD, a restart file which I am trying to make a pdb file from. I saw, online, that "ambpdb" would not work but that ptraj would. I tried this and it did write out a pdb file but the last 10-11 residues on terminus were placed away from the protein.

Any ideas on how to fix this? Is it something I am doing?

I am sending you the pdb file and the output which does say there were errors, but not what they were...Just "in reading the prmtop file".

Steve


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Received on Wed Jun 01 2011 - 11:00:05 PDT
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