CHARMM Development Project Forums User Discussion & Questions Parameter Set Discussion *** Topology file for AMP? ***

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...

GENER and PATCH are specific CHARMM commands, and are not used or recognized in the topology file; you must determine the equivalent NAMD commands (psfgen?) and how to use them.

The $600 fee is a terrific bargain, compared to the cost of buying CHARMm from Accelrys; because of the commercial variant, the academic version cannot be freely distributed.

Instead of using a TCL script, you could just make your PSF in charmm, and convert it to a NAMD format PSF using a utility on the NAMD website, I think it's called charmm2namd. You can do the same thing with a coordinate file (crd2pdb).

I'd recommend doing all your model building and analysis in CHARMM, it's much much easier than anything with tcl scripts.. part of the reason the 600$ is well worth it.