From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 15 2015 - 05:10:10 CST

On Wed, Jan 14, 2015 at 5:18 PM, Nathan K Houtz <nhoutz_at_purdue.edu> wrote:
> 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:

VMD does not know anything about molecules or atom types. all it does
is read the information that you provide in the files you read into
VMD and for files with limited information VMD uses some heuristics to
guess those missing parts (e.g. bonds from distances, elements/masses
from names). if you look at the topotools tutorials, you should have
already seen, that it is *your* job to provide the proper information,
e.g. through VMD scripting. this is doubly true, if the contents of
the file you provide do not conform to the conventions that VMD
applies. as with all heuristics, this can go wrong.

>
> LAMMPS data file. CGCMM style. atom_style molecular generated by VMD/TopoTools v1.2 on Wed Jan 14 16:53:20 -0500 2015

topotools v1.2 is *waaay* outdated. please update your VMD
installation to VMD 1.9.2, which includes the current version.

also, you are writing out a molecular atom_style data file, which does
not contain charges at all.

overall, i suggest you discuss these issues with your adviser.

axel.

> 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

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.