Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb

From: David A Case <>
Date: Wed, 10 Sep 2014 07:49:04 -0400

On Wed, Sep 10, 2014, wrote:
> There is problem when pdb file is created using "ambpdb" command. The ATOM
> numbers are correct but Water residues (WAT) are not numbered correctly.
> In the test.pdb file after resid 9999, residue numbering starts again with
> 0, 1, 2......3216.

There is no good answer here. ambpdb is following the PDB format requirements
that allow only 4 digits for the residue number. The result of "savepdb"
actually violates the PDB format, but may be more useful in some other
contexts. Since you have both formats available to you, choose the one that
best fits your needs.

The PDB itself is addressing this problem by abandoning the current 80-column
format, and moving to mmcif. But this will be a slow process, since many,
many current programs expect the 80-column format that is not suited for
systems with more than 10,000 residues.


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Received on Wed Sep 10 2014 - 05:00:03 PDT
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