AMBER Archive (2006)

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

From: Christophe Guilbert (
Date: Thu Jun 29 2006 - 20:28:31 CDT

Hi again,
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.

comand used for antechamber and parmcheck.
antechamber -nc -5 -rn lig -i liga_regul.pdb -fi pdb -o lig_bcc.mol2 -fo
mol2 -c bcc -j 4 -at gaff -pf y
parmchk -i lig_bcc.mol2 -f mol2 -o lig_bcc.frcmod

Christophe Guilbert, Ph.D.
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UCSF, Department of Pharmaceutical Chemistry
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