Re: alchemify with CMAP?

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Thu Apr 16 2009 - 19:21:51 CDT

Dear Sebastian,

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
it.

Thanks for raising this issue...
Jerome

On Thu, Apr 16, 2009 at 8:11 PM, Sebastian Stolzenberg
<s.stolzenberg_at_gmail.com> wrote:
> 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
> GLU2GLUP).
>
> 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,
> Sebastian
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:46 CST