Dear Murai
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
message was:
No bond types defined for the bond between
atoms /atom:NaSSs\[2\]\[2\]\[2\]/O3 \(type @/atom:GAFF/o\)
and /atom:NaSSs[2][2][2]/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.
Andrew