From e77d12fa33095a877e0e21e35ecb0c806b51f228 Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Thu, 13 Jun 2013 16:35:18 +0200
Subject: [PATCH] CSBackbone - more documentation
---
src/colvar/CS2Backbone.cpp | 8 +++----
user-doc/bibliography.bib | 46 ++++++++++++++++++++++++++++++++++++++
2 files changed, 50 insertions(+), 4 deletions(-)
diff --git a/src/colvar/CS2Backbone.cpp b/src/colvar/CS2Backbone.cpp
index 60879518d..d76703392 100644
--- a/src/colvar/CS2Backbone.cpp
+++ b/src/colvar/CS2Backbone.cpp
@@ -62,7 +62,7 @@ ALMOST 2.1 can be found in branches/almost-2.1/ and it can be compiled:
make
\endverbatim
-Once the code is compiled you should find the ALMOST library libAlm.a in src/lib/
+Once the code is compiled you should see the ALMOST library libAlm.a in src/lib/
Experimental chemical shifts must be provided for all the nuclei and the residues of the system of interest setting to 0 those
that are missing.
@@ -71,7 +71,7 @@ that are missing.
\verbatim
WHOLEMOLECULE ENTITY0=1-174
-cs: CS2BACKBONE ATOM=1-174 DATA data/ FF a03_gromacs.mdb FLAT 0.0 NRES 13 [ENSEMBLE]
+cs: CS2BACKBONE ATOM=1-174 DATA=data/ FF=a03_gromacs.mdb FLAT=0.0 NRES=13 [ENSEMBLE]
PRINT ARG=cs
\endverbatim
(See also \ref WHOLEMOLECULE)
@@ -269,8 +269,8 @@ PLUMED_COLVAR_INIT(ao)
checkRead();
log<<" Bibliography "
- <<plumed.cite("Camilloni C, Robustelli P, De Simone A, Cavalli A, Vendruscolo M, J. Am. Chem. Soc. 134, 3968 (2012)") <<"\n"
- <<plumed.cite("Kohlhoff K, Robustelli P, Cavalli A, Salvatella A, Vendruscolo M, J. Am. Chem. Soc. 131, 13894 (2009)") <<"\n";
+ <<plumed.cite("Kohlhoff K, Robustelli P, Cavalli A, Salvatella A, Vendruscolo M, J. Am. Chem. Soc. 131, 13894 (2009)")
+ <<plumed.cite("Camilloni C, Robustelli P, De Simone A, Cavalli A, Vendruscolo M, J. Am. Chem. Soc. 134, 3968 (2012)") <<"\n";
addValueWithDerivatives();
setNotPeriodic();
diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib
index 610db4c13..f970c08cd 100644
--- a/user-doc/bibliography.bib
+++ b/user-doc/bibliography.bib
@@ -1887,6 +1887,52 @@ number = {7},
pages = {2247--2254}
}
+@article{Kohlhoff:2009us,
+author = {Kohlhoff, KJ and Robustelli, Paul and Cavalli, Andrea and Salvatella, Xavier and Vendruscolo, Michele},
+title = {{Fast and accurate predictions of protein NMR chemical shifts from interatomic distances}},
+journal = {J. Am. Chem. Soc.},
+year = {2009},
+volume = {131},
+number = {39},
+pages = {13894--13895}
+}
+@article{Robustelli:2010dn,
+author = {Robustelli, Paul and Kohlhoff, Kai and Cavalli, Andrea and Vendruscolo, Michele},
+title = {{Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins}},
+journal = {Structure},
+year = {2010},
+volume = {18},
+number = {8},
+pages = {923--933},
+}
+@article{Camilloni:2012je,
+author = {Camilloni, Carlo and Robustelli, Paul and De Simone, Alfonso and Cavalli, Andrea and Vendruscolo, Michele},
+title = {{Characterization of the Conformational Equilibrium between the Two Major Substates of RNase A Using NMR Chemical Shifts.}},
+journal = {J. Am. Chem. Soc.},
+year = {2012},
+volume = {134},
+number = {9},
+pages = {3968--3971},
+}
+@article{Granata:2013dk,
+author = {Granata, Daniele and Camilloni, Carlo and Vendruscolo, Michele and Laio, Alessandro},
+title = {{Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics.}},
+journal = {Proc. Natl. Acad. Sci. U.S.A.},
+year = {2013},
+volume = {110},
+number = {17},
+pages = {6817--6822},
+}
+
+@article{Camilloni:2013hs,
+author = {Camilloni, Carlo and Cavalli, Andrea and Vendruscolo, Michele},
+title = {{Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins}},
+journal = {J. Phys. Chem. B},
+year = {2013},
+volume = {117},
+number = {6},
+pages = {1838--1843},
+}
--
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