VMD-L Mailing List
From: Nathan K Houtz (nhoutz_at_purdue.edu)
Date: Wed Jan 14 2015 - 16:18:42 CST
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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
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- Next in thread: Axel Kohlmeyer: "Re: using topotools: error in identifying atoms and dihedrals"
- Reply: Axel Kohlmeyer: "Re: using topotools: error in identifying atoms and dihedrals"
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