Dear all,
Since several people are also interested in the question I posted to
AMMRL below, I post the response I got. I want to thank all the people
who took the time responded to my inquiry.
1. MSpin:
##########
I've only used the trial version, but I've had success with Mestrenova's
MSpin module. It's really cool: you give it 3D coordinates (I think I
used pdb format), and it gives you predicted NMR-observable quantities.
Select two scalar-coupled 1H's, and it estimates the 3JHH value. Select
two 1H's, pick a field strength, choose a mixing time, and tell it
whether you're doing a NOESY or 1D NOE, and it estimates a correlation
time and NOE value. It's also set for small molecule RDC calculations.
Of course, it would be great if you could do restrained simulated
annealing, but it's not set up for that. I think Spartan can, but it may
be trouble - maybe not NMR-specific enough.
#########
2. ACD labs
ACD/Structure Elucidator offers some of the capabilities you requested
in the AMMRL post. Below is a publication that explains how the software
works to differentiate compounds using NOESY data.
Smurnyy, YD and Elyashberg, ME and Blinov, KA and Lefebvre, BA and
Martin, GE and Williams, AJ. Computer-aided determination of relative
stereochemistry and 3D models of complex organic molecules from 2D NMR
spectra. Tetrahedron 61(42):9980--9989, 2005.
<
http://www.acdlabs.com/publish/publ05/rsc.html> BibTeX
<javascript:bibpopup('_at_article%7bsmurnyy2005cad,%20%20title=%7b%7bComput
er-aided%20determination%20of%20relative%20stereochemistry%20and%203D%20
models%20of%20complex%20organic%20molecules%20from%202D%20NMR%20spectra%
7d%7d,%3cbr%3e%20%20author=%7bSmurnyy,%20Y.D.%20and%20Elyashberg,%20M.E.
%20and%20Blinov,%20K.A.%20and%20Lefebvre,%20B.A.%20and%20Martin,%20G.E.%
20and%20Williams,%20A.J.%7d,%3cbr%3e%20%20journal=%7bTetrahedron%7d,%3cb
r%3e%20%20volume=%7b61%7d,%3cbr%3e%20%20number=%7b42%7d,%3cbr%3e%20%20pa
ges=%7b9980--9989%7d,%3cbr%3e%20%20year=%7b2005%7d,%3cbr%3e%20%20publish
er=%7bElsevier%7d,%3cbr%3e%20%20url=%7b
http://www.acdlabs.com/publish/pu
bl05/rsc.html%7d%7d')>
3. Felix NMR 2007.
I believe these are the three solutions I received. I got a trial
license from Steve at Felix, but in the end, I did not go through it. I
contacted Accelrys, but was told no such module exists now. I also
talked with people working on protein area, and was told that it does
not worth the efforts because we have to manually assign each atom. In
the end, I just use molecular modeling to qualitatively analyze the
structure and the results seem to be what we expected, so I stopped
there.
Regards,
Wei Li
--------------------------------
Wei Li, Ph.D.
Associate Professor/Director of NMR Facility
University of Tennessee Health Science Center
847 Monroe Avenue, room 327
Memphis, TN 38163
901-448-7532 (PH)
http://www.uthsc.edu/pharmacy/pharmsci/faculty/wli/
<
http://www.uthsc.edu/pharmacy/pharmsci/faculty/wli/>
Email: wli_at_uthsc.edu <mailto:wli_at_uthsc.edu>
Or wli.uthsc_at_gmail.com <mailto:wli.uthsc_at_gmail.com> (for large
attachment file)
From: Li, Wei
Sent: Friday, June 03, 2011 6:02 PM
To: ammrl_at_ammrl.org
Subject: AMMRL: SIMPLE software for small molecular structure analysis
based on NOE and maybe coupling constants
Dear colleagues,
Many years ago I used Triad software from Tripos to calculate the small
molecular conformation based on NOE constraints. Unfortunately, it is no
longer available now. We now have some small organic molecules which
have two possible diastereomers, and we want to know which one is more
likely based on NOESY measurement. I am looking for a program that can
interact with a molecular model, assign the NOE peaks, use the assigned
volume as constraints, and calculate which structure would have less
distance violations. I don't want a fancy which people working in
protein areas use. Could anyone recommend a program that is suitable for
determining small molecular structure and relatively easy to use?
Thank you very much and you all have a great weekend.
Wei Li
--------------------------------
Wei Li, Ph.D.
Associate Professor and Director of NMR Facility
University of Tennessee Health Science Center
847 Monroe Avenue, room 327
Memphis, TN 38163
901-448-7532 (PH) 901-448-6828 (Fax)
http://www.uthsc.edu/pharmacy/pharmsci/faculty/wli/
Email: wli_at_uthsc.edu
Received on Thu Aug 04 2011 - 09:08:46 MST