I've come across an issue saving .mol2 ( @<TRIPOS> ) files.
MGL tools' PMV/ADT won't read them, babel/open babel issues a set of complaint and read errors.
If I am reading the format correctly then ...
In the atom content the columnation appears to be off after the X Y Z coordinates, the question marks under atom_type seem to throw a lot of scripts (not surprising).
I'm not quite sure what the issue is, but it occurs when saving peptides and molecules built by a mouse or script as well as RCSB downloaded structures. seems the same on all builds and machines I've tried (listed at bottom)
thanks for your time
# created with PyMOL
57 57 0 0 0
1 N 0.394 -2.167 -1.142 ?? 1.000
2 CA 0.891 -0.794 -1.142 ?? 1.000
3 C 2.400 -0.765 -1.142 ?? 1.000
4 O 3.074 -1.654 -0.600 ?? 1.000
5 CB 0.286 0.038 0.061 ?? 1.000
6 CG1 -1.272 -0.010 0.168 ?? 1.000
saved from pymol 1.6 https://www.dropbox.com/s/jlpwa2lsub5ez8g/IPR.mol2
babel pipes https://www.dropbox.com/s/ruh23hcxfmbv0z8/babelmol2_mol2.txt
babel out https://www.dropbox.com/s/3p41lkvybdlwhwc/IPR_mol2mol2_babeled.mol2
tripos mol2 format pdf http://www.tripos.com/data/support/mol2.pdf
dell T3600 e5-1650
w/ quadro 600 xUbuntu 13.04 pymol 1.6.0 from source w/build_seq.py and seq_convert.py
1.5.2 from package (and lots of plugins)
lenovo t420 nvs 400
windows 7 1.4.? (not sitting at it while typing) pre-built many plugins
also xUbuntu 12.04 1.4 from package and 1.6 from source (w/nvidia-bumblebee, and just intel graphics)