"No bond types defined" for atoms in OPLSAA (since 2023 update)

[pbriml]

Hi Andrew,

I am trying to build simulations of anion exchange membranes (like PiperION) which contain para-terphenyl and biphenyl units. The examples containing benzene you have linked here unfortunately no longer run and I receive the following error:

Looking up bond types according to atom type
bonds_by_type.py v0.13.0 2020-11-04 

Error: No bond types defined for the bond between
       atoms $/atom:benzenes[0][0][0]/c1 (type @/atom:OPLSAA/145_b016_a016_d016_i016)
         and $/atom:benzenes[0][0][0]/h1 (type @/atom:OPLSAA/146_b017_a017_d017_i017)

       (If you are using a force field, then it probably means that you made a
        mistake choosing at least one of these two @atom types from the list
        of available atom types supplied by the force field.  To fix it, edit
        the corresponding lines in the "Data Atoms" section of your LT file.)

`

This also happens for the atoms in the ethylene molecule. I have updated my moltemplate since the changes you've made in the OPLS-AA directories, but maybe something is wrong on my end.

Thanks!

[jewettaij]

Hi pbriml

I'm sorry about the problems you experienced. The @atom types have changed completely since "oplsaa.lt" was updated to the 2023 version. I was afraid that this would cause backward compatibility problems for people, but the 2023 version is significantly better than the older 2008 version in several ways. (Better force-field parameters, updated impropers, easier-to-understand atom types.)

In the future, it may change again, whenever the Jorgensen group releases new .par and .sb files in the public domain.

You have two choices:

• update the @atom type numbers in your molecules, or
• use the old (2008) version of the OPLSAA force field instead. (To do that, replace "import oplsaa.lt" with "import oplsaa2008.lt" everywhere it appears in your .lt files. If you are using the old LOPLS file, "loplsaa.lt", then that file also needs to be changed to "loplsaa2008.lt". That should be all you need to do.)

I am reopening this issue so that other people can see my response.

[pbriml]

Hi Andrew,

Thank you for your response! I was able to get it to work earlier by uninstalling moltemplate and re-installing. Everything is now functional for me.