[AMBER-Developers] antechamber default residue name

From: Timothy J Giese <timothyjgiese.gmail.com>
Date: Tue, 07 Jan 2014 13:22:57 -0500

I feel like something has changed with antechamber... although I'm not immediately seeing anything in the git revisions that would change this. Maybe I'm somehow using it differently (?). I don't know. Here's what I'm seeing though.

I'm using 0541586bf4052136921191596329ba34a466c65f
configured with gnu
gcc (GCC) 4.6.3 20120306 (Red Hat 4.6.3-2)

I have a pdb file generated by openbabel (attached).

When I run

antechamber -i PM3BP.U.pdb -fi pdb -o PM3BP.U.mol2 -fo mol2 -c bcc -s 2 -nc 0

It produces PM3BP.U.mol2, but the residue name is left blank in the mol2 file.

When I run parmchk, I get a memory allocation error

parmchk -i PM3BP.U.mol2 -f mol2 -o PM3BP.U.frcmod
memory allocation error for *bond_array

When I load the mol2 file into tleap, it dies with

Loading parameters: /home/giese/devel/git/Programs/Amber11/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.7, Nov 2013)
Loading Mol2 file: ./PM3BP.U.mol2
Reading MOLECULE named 12 12 1 0 0
Fatal Error: last line read: 1 C -1.2390 -0.4190 0.0010 c 1 0.803500

The solution is to explicitly specify the -rn flag when using antechamber.
When -rn is explicitly used, parmchk no longer produces a memory allocation error and tleap runs fine.

I was surprised by this because I've never had to use that flag before.
antechamber -h says:
-rn residue name, overrides input file, default is MOL
which suggests that the residue name should default to MOL.

I'm not seeing anything weird in the pdb file that would blank it.
...but maybe there is (?)


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Received on Tue Jan 07 2014 - 10:30:02 PST
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