Converting molecular structure to LAMMPS data file form via VMD topotools

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)

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”

There is a good reason why this command is called _guess_dihedrals. The Topotools package is completely ignorant of the force field and thus may require additional tweaks. Your case is one of those. You have to add the missing dihedrals manually. Charmm has those strange definitions mostly for historical reasons due to limitations of their software.