msi2lmp tool error

Dear all,
Happy new year!

I want to use msi2lmp tool, in order to, i have created msi files (.car & .mdf) by material studio. the only molecule in my system is 4-monomer polymer (pmma). the used force field is PCFF (class 2) to create msi files. when use msi2lmp to create input and data files for lammps, it get to error! the following error:

Polypmma-pcff.car (12.3 KB)

Polypmma-pcff.mdf (12.9 KB)

Dear all,
Happy new year!

I want to use msi2lmp tool, in order to, i have created msi files (.car &
.mdf) by material studio. the only molecule in my system is 4-monomer
polymer (pmma). the used force field is PCFF (class 2) to create msi files.
when use msi2lmp to create input and data files for lammps, it get to
error! the following error:

-----------------------------
Forcefield: Class II
Forcefield file name: ../frc_files/pcff.frc
Output is recentered around geometrical center
Output contains style flag hints
System translated by: 0 0 0
Reading car file: pmma-pcff.car
Reading mdf file: pmma-pcff.mdf

Building internal coordinate lists

Reading forcefield file

Get force field parameters for this system
Unable to find angle data for oc coh oh
----------------------------

​this means that either your atom typing is incorrect or that your system
needs parameters that the bundled pcff force field file does not support.
please note that msi2lmp only bundles parameter sets that are freely
available and not those covered by commercial licenses.

when i run the most recent version of msi2lmp on your files, i get
additional warnings which suggest that your atom typing may not be 100%
accurate.

Building internal coordinate lists
WARNING inconsistent # of connects on atom 2 type c
WARNING inconsistent # of connects on atom 18 type c
WARNING inconsistent # of connects on atom 33 type c
WARNING inconsistent # of connects on atom 48 type c
WARNING inconsistent # of connects on atom 63 type c
WARNING inconsistent # of connects on atom 78 type c
WARNING inconsistent # of connects on atom 93 type c
WARNING inconsistent # of connects on atom 108 type c
WARNING inconsistent # of connects on atom 123 type c
WARNING inconsistent # of connects on atom 139 type c

​axel.​

If you use this command, the file will be created; however, you need to make sure that the created file is acceptable for your simulation purposes, while it lacks some of the parameters.

msi2lmp.exe Polypmma-pcff -class II -frc pcff -ignore

If you use this command, the file will be created; however, you need to
make sure that the created file is acceptable for your simulation purposes,
while it lacks some of the parameters.

​this is definitely *not* the case if the missing parameters are for an
angle type (or bond or dihedral). apart from that, it is often not very
straightforward to see, if a simulation will produce acceptable results
when missing parameters are set to zero. the effects can be quite subtle,
yet the resulting simulations are bogus nevertheless.

as i wrote in my previous e-mail, the warnings printed by the recent
version msi2lmp, however, make it very likely that there is an error in the
assignment of atom types, e.g. from connecting monomers without changing
the atom types of the atoms forming the connecting bond. this in turn
means, that there are probably *more* atoms that are mistyped, yet they
won't get listed if their connectivity doesn't change.

msi2lmp.exe Polypmma-pcff -class II -frc pcff* -ignore*

​this is dangerous advice. ​​using the ignore flag​
​ is really only acceptable for the ​specific class2 force field terms like
bond-bond, bond-angle, angle-angle-torsion, end-bond-torsion,
middle-bond-torsion, bond-bond-1-3, angle-torsion and angle-angle. ...and
even then i would be worried.

people should only ignore warnings and errors, if they know *exactly* what
is causing them and understand that they can safely ignore them. if in
doubt, assume that it is wrong, not right.

axel.