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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Received on Sun Jul 09 2006 - 06:07:09 PDT
