From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Thu Apr 16 2009 - 19:21:51 CDT
You make a very good point. Alchemify was written back in the days
when I didn't worry about CMAP that much. It's silly, because the CMAP
section should be copied properly - it's just that the word "CMAP"
gets deleted from the first line.
Now, this should not be a problem from now on, since NAMD 2.7 makes
Alchemify obsolete - everything is handled internally. At this point I
should just change all the documentation to tell people *not* to use
Thanks for raising this issue...
On Thu, Apr 16, 2009 at 8:11 PM, Sebastian Stolzenberg
> Dear Jerome,
> from a CMAP-equilibrated system, I have prepared a CMAP FEP initial
> structure (psf/pdb), using my own CMAP-hybrid-topology definitions (for
> In this regard, can "alchemify" handle CMAP? The reason I wanted to
> double-check with you is that in your "alchemify" C code, I found commands,
> writing out "PSF" as first line, regardless of whether the first input psf
> line was "PSF" or "PSF CMAP".
> Thanks for your help,
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