Hello Ben,
The anger, well yes, but it is one of those bodgable situations.
There is indeed a hard-coded limit of 8 bonds that shall not be exceeded, I
confess I found this out a scant hour or two after posting to the message
board. It is in the atom file in the source for leap. Changing this to 16
seemed reasonable and afterwards recompiled without issue. It seems sander
and pmemd are both fine with 10-bonded species and I get a nice happy
accordian breathing ferrocene.
pert=true gives some syntax error, setting it for all atoms (without equals
sign) works, in that it sets the property for all atoms. However, the pert
setting (which can be seen using desc) does not override the hard coded
limits of the program, simply the soft limits for that atom type (so you
can make banana bonds if you wanted).
Just replying for anyone who has had a similar issue to google in the
future, and to say my thanks!
-David
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 06 2017 - 03:30:03 PDT
