AMBER Archive (2006)

Subject: Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars.

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 05 2006 - 16:31:14 CDT

On Thu, Jun 29, 2006, Christophe Guilbert wrote:

> Here is small bug that I found when you try to write a pdb file using tleap
> in amber 8.0 the bug concerns some formatting problem when the pdb file
> contain 4 letters atom name. when you run a ligand (see attachment ) with
> antechamber -> parmcheck -> tleap , tleap does not write the pdb file
> correctly , atom which has 4 characters names (in this example) are not
> interpreted correctly and named differently in the pdb file by tleap.

I don't see any bug. You don't say what the output from tleap was, or what
you thought the error was.

Note that the liga_regul.pdb file you used as input does not conform to pdb
standards, which state that the two character element name must be
right-justified in columns 13-14. Antechamber still reads it OK, but when
tleap writes out the pdb file, it follows the Brookhaven standard.

Thus, if you have "HN21" in columns 13-16 of your pdb file, tleap correctly
translates this to "1HN2" as required by pdb syntax.

If you want to keep the original names, you can use ambpdb with the -aatm
flag -- see the ambpdb section of the manual (p. 284 for Amber 9) for a fuller
discussion of atom names in pdb files.

....regards...dac

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