PREPARING THE INPUT FILE

Hi Lammps users,

I wanted to use the oplsaa.frc file while preparing the input file for lammps (while using the msi2lmp tools)

But, got the following error

"Reading forcefield file
Inconsistent parameter file.
Expected: ‘r-eps’ type non-bonded data, found: A-B"

For benzene derivatives, papers suggest that oplsaa.frc is the best.

However, when I use cff91.frc, I get an output with NO parameters in it.

Like this…

Pair Coeffs # lj/class2/coul/long

1 0.0000000000 0.0000000000 # H
2 0.0000000000 0.0000000000 # C
3 0.0000000000 0.0000000000 # N
4 0.0000000000 0.0000000000 # O

Bond Coeffs # class2

1 0.0000 0.0000 0.0000 0.0000 # H-C
2 0.0000 0.0000 0.0000 0.0000 # C-C
3 0.0000 0.0000 0.0000 0.0000 # C-N
4 0.0000 0.0000 0.0000 0.0000 # H-N
5 0.0000 0.0000 0.0000 0.0000 # H-O

Angle Coeffs and so on…

How to proceed?

Thanks,

Kulkarni.R

Hi Lammps users,

I wanted to use the oplsaa.frc file while preparing the input file for
lammps (while using the msi2lmp tools)

But, got the following error

"Reading forcefield file
Inconsistent parameter file.
Expected: 'r-eps' type non-bonded data, found: A-B"

that suggests you are using incorrect/inconsistent command line flags,
and possibly not the latest version of the code.

For benzene derivatives, papers suggest that oplsaa.frc is the best.

if you look at the oplsaa.frc file bundled with msi2lmp, you should
see, that it does not contain any parameters for aromatic carbon atom
types. if you want to have it to support aromatic hydrocarbons, you'll
have to add the parameters for it, as well.

However, when I use cff91.frc, I get an output with NO parameters in it.

Like this..

Pair Coeffs # lj/class2/coul/long

   1 0.0000000000 0.0000000000 # H
   2 0.0000000000 0.0000000000 # C
   3 0.0000000000 0.0000000000 # N
   4 0.0000000000 0.0000000000 # O

Bond Coeffs # class2

   1 0.0000 0.0000 0.0000 0.0000 # H-C
   2 0.0000 0.0000 0.0000 0.0000 # C-C
   3 0.0000 0.0000 0.0000 0.0000 # C-N
   4 0.0000 0.0000 0.0000 0.0000 # H-N
   5 0.0000 0.0000 0.0000 0.0000 # H-O

Angle Coeffs and so on.............

How to proceed?

that means, that you have been ignoring warnings from the msi2lmp
output and/or told it to ignore them.
however, the warnings told you, that you atom types, don't match with
the type names of the force field.

the comments confirm this. you have not typed your atoms at all, but
simply labeled them by the element. below is a part of the non-bonded
atom types. you can see that the force field file bundled with msi2lmp
knows about 27 different types of carbon atoms.

!Ver Ref Type Mass Element Connection Comment
!---- --- ---- ---------- ------- -----------------------------------------
1.0 1 c 12.01115 C 4 generic SP3 carbon
1.0 1 c3 12.01115 C 4 sp3 carbon with 3 hHs 1 heavy
1.0 1 c2 12.01115 C 4 sp3 carbon with 2
H's, 2 Heavy's
1.0 1 co 12.01115 C 4 sp3 carbon in acetals
1.0 1 c3m 12.01115 C 4 sp3 carbon in 3-membered ring
1.0 1 c4m 12.01115 C 4 sp3 carbon in 4-membered ring
2.0 1 coh 12.01115 C 4 sp3 carbon in
acetals with hydrogen
2.0 2 c3h 12.01115 C 4 sp3 carbon in
3-membered ring with hydrogens
2.0 2 c4h 12.01115 C 4 sp3 carbon in
4-membered ring with hydrogens
1.0 1 c1 12.01115 C 4 sp3 carbon with 1 H 3 heavies
1.0 1 ca 12.01115 C 4 general amino acid
alpha carbon (sp3)
1.0 1 cg 12.01115 C 4 sp3 alpha carbon in glycine
1.0 1 c= 12.01115 C 3 non aromatic end
doubly bonded carbon
2.0 3 c=1 12.01115 C 3 non aromatic, next
to end doubly bonded carbon
2.0 3 c=2 12.01115 C 3 non aromatic doubly
bonded carbon
2.0 4 c* 12.01115 C 3 carbon in carbonyl
group, non_amides
1.0 1 c" 12.01115 C 3 carbon in carbonyl
group, non_amides
1.0 1 c' 12.01115 C 3 carbon in carbonyl
group of amides
1.0 1 cp 12.01115 C 3 sp2 aromatic carbon
1.0 1 c5 12.01115 C 3 sp2 aromatic carbon
in 5-membered ring
1.0 1 c- 12.01115 C 3 C in charged carboxylate
1.0 1 cr 12.01115 C 3 C in neutral arginine
1.0 1 c+ 12.01115 C 3 C in guanidinium group
1.0 1 cs 12.01115 C 3 sp2 aromatic carbon
in 5 membered ring next to S
1.0 1 ci 12.01115 C 3 sp2 aromatic carbon
in charged imidazole ring (His+)
1.0 1 ct 12.01115 C 2 sp carbon
involved in a triple bond
2.0 6 ct2 12.01115 C 2 sp carbon in CO2

but that is only part of the story. in addition to correctly assigning
atom types, you'll also have to assign (partial) charges to atoms,
which are determined by the kind of functional group you have or
through some increment system (which is what OPLS-AA uses). there are
a some examples for how to do this with OPLS-AA for aliphatic
hydrocarbons here:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2

for msi2lmp, the atom typing is usually done in materials studio.
before writing out the .mdf and .car files.

axel.