Dear LAMMPS users,
Hi, I’m trying to convert an ethylene carbonate structure to LAMMPS data file form via VMD topotools.
I know the coordinates of atoms and partial charges.
First, I’ve followed nice series of tutorials provided by Dr. Kohlmeyer to learn and practice.
Then I made a coordinate file (XYZs) by myself and converted it into LAMMPS data file.
However I get lack of number of the dihedrals compare to the literature I’m referring.
Any suggestions to precisely convert coordinate information into LAMMPS data file format?
The TCL script I’ve used for dihedral is “topo guessdihedrals”
Missing dihedral types are especially the ones having periodicity like below (I only get 1 O-C-OS-C3 dihedral)
Type 1 O-C-OS-C3; periodicity 2
Type 2 O-C-OS-C3; periodicity 1
I’ve attached the coordinate file of energy minimized ethylene carbonate for check.
10
EC test1
C1 -0.36900 1.46500 0.09900
O1 -0.28300 0.27400 0.14900
O2 -1.49000 2.17800 0.40700
O3 0.63800 2.30400 -0.27300
C2 -1.28800 3.56300 0.06900
C3 0.23700 3.66900 -0.04900
H1 -1.71300 4.18000 0.86800
H2 -1.80300 3.77000 -0.87800
H3 0.71200 4.02500 0.87500
H4 0.57400 4.27300 -0.89800
Furthermore, maybe not related to LAMMPS, I’m trying to get force field parameters based on generalized AMBER force field by Antechamber.
I can also convert the coordinate file simultaneously into pdb file and use it to obtain ‘frcmod’ file from Antechamber.
However, the Antechamber can only figure nothing but the number of bonds so I get none force field parameters.
I guess the quality of pdb file I converted is causing the trouble.
How can I overcome this? A firm pdb file from RCSB PDB works fine.
PDB file converted from coordinate
CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 1
ATOM 1 C1 X 1 -0.369 1.465 0.099 0.00 0.00 C
ATOM 2 O1 X 1 -0.283 0.274 0.149 0.00 0.00 O
ATOM 3 O2 X 1 -1.490 2.178 0.407 0.00 0.00 O
ATOM 4 O3 X 1 0.638 2.304 -0.273 0.00 0.00 O
ATOM 5 C2 X 1 -1.288 3.563 0.069 0.00 0.00 C
ATOM 6 C3 X 1 0.237 3.669 -0.049 0.00 0.00 C
ATOM 7 H1 X 1 -1.713 4.180 0.868 0.00 0.00 H
ATOM 8 H2 X 1 -1.803 3.770 -0.878 0.00 0.00 H
ATOM 9 H3 X 1 0.712 4.025 0.875 0.00 0.00 H
ATOM 10 H4 X 1 0.574 4.273 -0.898 0.00 0.00 H
END
Thank you.
EC_3.pdb (877 Bytes)
EC_3.xyz (332 Bytes)
ECtodata_3.tcl (4.05 KB)