From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Mon Apr 20 2009 - 11:42:05 CDT
ERRATUM: I said that alchemify was obsolete - that is not quite true
yet. The code that takes care of everything internally exists, but is
not yet part of the official CVS tree (or of 2.7b1, for that matter).
So yes, Alchemify is still needed, at least when mutating part of a
bonded structure (e.g. point mutation in a peptide). If only whole
molecules (or ions) appear and disappear, then it is not necessary.
Hopefully the patch will make it into 2.7 final, in which case what I
said in that previous message will technically be true :-)
2009/4/17 Jerome Henin <jhenin_at_cmm.chem.upenn.edu>:
> Hi Sébastien,
> You can check that the "NCRTERM" section at the end of the file is
> intact. Actually, looking at the source code, it seems that NAMD
> ignores the CMAP keyword on the first line anyway, so as log as the
> last section is present, cross-terms should be properly included. To
> check for this, just look at the "Structure Summary" section of the
> NAMD log file.
> 2009/4/17 Sébastien Légaré <Sebastien.Legare_at_rsvs.ulaval.ca>:
>> Hi Jerome
>> I completely missed this. Just to be sure, adding the word "CMAP" on the first
>> line of the psf generated by Alchemify will get CMAP included right? Would
>> something more be missing?
>> On April 16, 2009 08:21:51 pm you wrote:
>>> 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
>>> Thanks for raising this issue...
>>> 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
>> Sébastien Légaré
>> Ph. D. Student
>> Laval University
>> Quebec, Canada, G1V 0A6
>> 418-656-2131 #11577
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