From: Nathan K Houtz (nhoutz_at_purdue.edu)
Date: Wed Jan 14 2015 - 16:18:42 CST

Hello all,

I'm attempting to generate a LAMMPS input script for my advisor. I'm learning from Dr. Alex Kohlmeyer's tutorial here: http://pubchem.ncbi.nlm.nih.gov/compound/2-Butynoic_acid#section=Top. What I want to do with VMD is prepare a box of tetrolic acid (TTA) (aka 2-butynoic acid: http://pubchem.ncbi.nlm.nih.gov/compound/2-Butynoic_acid#section=Top). Unfortunately, VMD seems to be incorrectly identifying the fourth carbon (bonded to both the oxygen and the OH group) as an oxygen atom with no charge. It also fails to identify the improper dihedral with that same atom being the central atom. A sample of the output looks like this:

LAMMPS data file. CGCMM style. atom_style molecular generated by VMD/TopoTools v1.2 on Wed Jan 14 16:53:20 -0500 2015
 2160 atoms
 1944 bonds
 2592 angles
 1728 dihedrals
 0 impropers
 6 atom types
 7 bond types
 8 angle types
 6 dihedral types
 0 improper types
 -20.076023 20.664032 xlo xhi
 -22.231997 23.007997 ylo yhi
 -14.019025 14.001054 zlo zhi

# Pair Coeffs
#
# 1 CT
# 2 CZ
# 3 HC
# 4 HO
# 5 O
# 6 OH

# Bond Coeffs
#
# 1 CZ-O
# 2 CT-CZ
# 3 HO-OH
# 4 O-O
# 5 O-OH
# 6 CZ-CZ
# 7 CT-HC

# Angle Coeffs
#
# 1 CZ-O-O
# 2 CZ-O-OH
# 3 CZ-CT-HC
# 4 HO-OH-O
# 5 O-O-OH
# 6 CZ-CZ-O
# 7 CT-CZ-CZ
# 8 HC-CT-HC

# Dihedral Coeffs
#
# 1 CZ-O-OH-HO
# 2 O-O-OH-HO
# 3 CZ-CZ-O-O
# 4 CZ-CZ-O-OH
# 5 CT-CZ-CZ-O
# 6 HC-CT-CZ-CZ

 Atoms

1 1 1 -18.236025 -20.571995 -11.009017 # CT TTA
2 1 2 -17.356035 -19.491997 -11.479018 # CZ TTA
3 1 2 -16.616014 -18.611998 -11.859023 # CZ TTA
4 1 5 -15.726030 -17.561996 -12.309020 # O TTA
5 1 5 -14.586016 -17.741997 -12.719024 # O TTA
6 1 6 -16.266008 -16.321997 -12.209014 # OH TTA
7 1 4 -15.616014 -15.691998 -12.479033 # HO TTA
8 1 3 -19.076021 -20.131996 -10.469024 # HC TTA
9 1 3 -18.596010 -21.141998 -11.869018 # HC TTA
10 1 3 -17.676027 -21.231997 -10.349013 # HC TTA