Thanks for your patience. You do have a problem in your .LT
files. However moltemplate fails to correctly diagnose the problem.
Moltemplate complained about the wrong pair of atoms. The error
No bond types defined for the bond between
atoms /atom:NaSSs\[2\]\[2\]\[2\]/O3 \(type @/atom:GAFF/o\) and /atom:NaSSs/Na1 (type @/atom:GAFF/na)
However the "gaff.lt" file DOES define a bound between these two
atom types. Printing out a misleading error message is less than
helpful. Sorry about that.
I have fixed the bug in moltemplate (v1.33) and will post the
correction (v1.34) at moltemplate.org in the next few days. The
correct error message should be:
Error: No bond types defined for the bond between
atoms /atom:nass/C5 \(type @/atom:GAFF/ca\) and /atom:nass/H8 (type @/atom:GAFF/hc)
At least one of those two atom types is incorrect. Please change
either of these atom types (either @atom:ca @atom:hc). You also tried
to define a bond between atoms of type @atom:ca and @atom:s2. One of
these two atom types is also incorrect.
Check the "Data Bonds By Type" section of the "gaff.lt" file for a
list of acceptable atom types which can be bonded together. (A more
detailed explanation is included below.)
Thank you very much for reporting this issue to me. I think this
bug could effect a lot of people using either GAFF or OPLSAA. It's
only by reporting difficulties like this that the software will get
better. I really appreciate it.