Now I understand that altering ADE by the patch method is the way to go. Thank you for explaining this thoroughly.
That leads me to my next question: What is the syntax for embedding these patch commands into a tcl script readable by VMD instead of as CHARMM command input?
Here's the reason I ask this. I know this is a CHARMM forum that's not specifically dedicated to other software that uses CHARMM parameters, such as VMD, but from what I can tell from charm.org, the makers of CHARMM charge a $600 licensing fee for their command line-driven program. If there's another way to generate the relatively small quantity of code I apparently need to accomplish this patch, that would of course be optimal.
I'll keep trying variations on the earlier poster's GENE and PATC phrases with "3ter" and "5pho," but haven't had any luck so far, so if anyone knows the proper few lines of text to append to the ADE topology entry, that would be great.
You've been very helpful so far. Thanks in advance...