Re: [AMBER] Bug in tleap savemol2?

From: Jason Swails <>
Date: Wed, 23 Jul 2014 10:39:24 -0700

On Jul 23, 2014, at 9:41 AM, David Minh <> wrote:

> Hi all,
> I’m trying to set up a ‘pipeline’ that uses pdb2pqr to set receptor protonation states and then AmberTools to prepare prmtop and mol2 files. The mol2 files will be used in UCSF DOCK. I am using the following script in tleap:
> source leaprc.ff14SB
> set default PBRadii bondi
> # Receptor
> protein = loadpdb 3cqwA.0.amber.pqr
> saveamberparm protein 3cqwA.0.prmtop 3cqwA.0.inpcrd
> savepdb protein 3cqwA.0.amber.pdb
> savemol2 protein 3cqwA.0.mol2 0 # default atom types, seems to have a bug
> quit
> This successfully generates prmtop, inpcrd, and pdb files. However, tleap crashes at the end of this script:
> ...
> Writing pdb file: 3cqwA.0.amber.pdb
> Converting N-terminal residue name to PDB format: NARG -> ARG
> Converting C-terminal residue name to PDB format: CTHR -> THR
> Writing mol2 file: 3cqwA.0.mol2
> /Users/dminh/Installers/amber14/bin/tleap: line 17: 1183 Abort trap: 6 $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
> There is no further information in leap.log. Any ideas or suggestions?

Maybe the PQR file doesn't adhere to the PDB standard enough. Keep in mind that PQR files are whitespace-delimited, whereas PDB files are not. They were designed to be very similar, but it's possible the PDB parser isn't handling your PQR quite right.

I would suggest converting your PQR file to a PDB file and using that. If that still doesn't work, you can post your input structure here and someone can take a look at it.

As a workaround, you can use ambpdb or cpptraj to write a mol2 file from your prmtop.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jul 23 2014 - 11:00:02 PDT
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