read_data error, AngleCoeffs

Hello,

I am having an issue starting my LAMMPS simulations that I have not seen before. I generated a .data file using charmm2lammps.pl, which previously has worked well. As far as I can tell, my files conform to the required formatting. Now, when beginning my simulation, I get the following error:

Reading data file …
orthogonal box = (-450 -450 -20.74) to (450 450 879.26)
4 by 4 by 4 MPI processor grid
reading atoms …
16182 atoms
scanning bonds …
3 = max bonds/atom
ERROR: Unexpected end of AngleCoeffs section (…/read_data.cpp:1798)
Last command: read_data Fragment4_Implicit.data

My input file is below:

Created by charmm2lammps v1.9.1 on Thu May 24 15:49:23 EDT 2018

units real
neigh_modify delay 2 every 1

atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic

pair_style lj/charmm/coul/charmm/implicit 8.0 12.0 7.0 9.0
pair_modify mix arithmetic
kspace_style pppm 1e-4

read_data Fragment4_Implicit.data

special_bonds charmm
thermo 10
thermo_style multi
timestep 1.0

Below is what is likely the relevant section of my data file:

Angle Coeffs # charmm

1 120 116.7 0 0 # CN1 CN3T CN3
2 38 118.7 0 0 # CN1 CN3T CN9
3 70 119.6 0 0 # CN1 CN5G CN5
4 125 129 0 0 # CN1 CN5G NN4
5 50 124.1 0 0 # CN1 NN2 CN3
6 45 120 0 0 # CN1 NN2 CN7B
7 70 131.1 0 0 # CN1 NN2G CN2
8 45 113.3 0 0 # CN1 NN2G HN2
9 50 130.2 0 0 # CN1 NN2U CN1T
10 40.5 115.4 0 0 # CN1 NN2U HN2


116 130 123.8 0 0 # NN3 CN1 ON1C
117 60 133 0 0 # NN3A CN4 NN3A
118 80 104.3 0 0 # ON2 P2 ON2
119 88.9 111.6 0 0 # ON2 P2 ON3
120 104 120 0 0 # ON3 P2 ON3

Angles


Any help correcting this error will be hugely appreciated!

Hello,

I am having an issue starting my LAMMPS simulations that I have not seen
before. I generated a .data file using charmm2lammps.pl, which previously
has worked well. As far as I can tell, my files conform to the required
formatting. Now, when beginning my simulation, I get the following error:

​[...]​

Below is what is likely the relevant section of my data file:

​this information is useless without also the header file.
...and altogether a​ report like this is useless without specifying the
LAMMPS version you are using.

​beyond that, it would be best if you would construct a minimal (just a few
hundred atoms) test case that has the same issue and then provide all files
you need to run this and the exact command lines and output from all of
those commands. that way it is possible to try and reproduce the workflow
and check carefully at which step things go awry.

axel.​

It indicates you have more than 120 angle types in the header section of the topology file, however, there are 120 angle coefficients.

Sanjib

Hello,
I apologize for the oversights. I am using LAMMPS 11 Aug 2017.
Header:

LAMMPS data file. CGCMM Style. atom_style full. Created by charmm2lammps v1.9.1 on Tue May 29 10:48:45 EDT 2018

16182 atoms
17454 bonds
31707 angles
50471 dihedrals
1412 impropers

37 atom types
60 bond types
120 angle types
220 dihedral types
10 improper types

-450 450 xlo xhi
-450 450 ylo yhi
-20.74 879.26 zlo zhi

My number of angle types matches the number of entries in Angle Coeffs section.

I have duplicated the issue for a system with just 252 atoms. Relevant files are attached. The PSF file was generated with the PSF generator within VMD (CHARMM all27_na topology), and then files converted to LAMMPS input and data using charmm2lammps.pl.

Thanks again for your time. Do let me know if I’m leaving out some obvious information, I’m relatively new to LAMMPS.

Short.in (1.04 KB)

Short.out (907 Bytes)

Short.data (160 KB)

my_duplex_short_autopsf.psf (59.5 KB)

Hello,
I apologize for the oversights. I am using LAMMPS 11 Aug 2017.

​please update.​

Header:

LAMMPS data file. CGCMM Style. atom_style full. Created by charmm2lammps
v1.9.1 on Tue May 29 10:48:45 EDT 2018

       16182 atoms
       17454 bonds
       31707 angles
       50471 dihedrals
        1412 impropers

          37 atom types
          60 bond types
         120 angle types
         220 dihedral types
          10 improper types

        -450 450 xlo xhi
        -450 450 ylo yhi
      -20.74 879.26 zlo zhi

My number of angle types matches the number of entries in Angle Coeffs
section.

​no, it doesn't. while the list starts with type 1 and ends with type 120,
there are types missing. i.e. types 65, ​78

​axel.​

Two angle types are missing in the ‘Angle Coeffs’ section. There are coefficients for 118 angle types.