acid residues in the coarse-grained united residue (UNRES) force field.
{\it J. Chem. Theory Comput.}, {\bf 2014}, 10, 2194-2203.
+\bibitem{sieradzan_2015}
+A.K. Sieradzan, P. Krupa, H.A. Scheraga, A. Liwo, C. Czaplewski.
+Physics-based potentials for the coupling between backbone- and
+side-chain-local conformational states in the united residue
+(UNRES) force field for protein simulations.
+{\it J. Chem. Theory Comput.}, {\bf 2015}, 11, 817-831.
+
+\bibitem{krupa_2017}
+P. Krupa, A. Ha"labis, W. "Rmudzi"nska, S. O"ldziej, H.A. Scheraga, A. Liwo.
+Maximum Likelihood Calibration of the UNRES Force Field for
+Simulation of Protein Structure and Dynamics.
+\textit{J. Chem. Inf. Model}. \textbf{2017}, 57, 2364-2377
+
+\bibitem{karczynska_2018}
+A.S. Karczy"nska, M.A. Mozolewska, P. Krupa, A. Gie"ldo"n, A. Liwo, C. Czaplewski.
+Prediction of protein structure with the coarse-grained UNRES
+force field assisted by small X-ray scattering data and
+knowledge-based information.
+\textit{Proteins: Struct. Func. Bioinfo.}, \textbf{2018}, 86 (S1), 228-239. %DOI: 10.1002/prot.25421.
+
+\bibitem{czaplewski_2018}
+C. Czaplewski, A. Karczy"nska, A.K. Sieradzan, A. Liwo.
+UNRES server for physics-based coarse-grained simulations and prediction
+of protein structure, dynamics and thermodynamics.
+\textit{Nucleic Acids Research}, \textbf{2018}, 46, W304-W309.
+
\end{thebibliography}
\endgroup
THETPARPDB thetaml.5parm\\
ROTPARPDB scgauss.parm
-For CSA, the best force field is 4P. For MD, the 1L2Y\_1LE1 force field is best for
+For CSA, the best force field is 4P. For MD, the E0LL2Y force field is best for
ab initio prediction but provides medium resolution (5 A for 60-residue proteins) and
overemphasizes $\beta$-structures and has to be run with secondary-structure-prediction
information. For prediction of the structure of mostly $\alpha$-protein, and for running
dynamics of large proteins, the best is the GAB force field. All these force fields
were trained by using our procedure of hierarchical optimization \cite{oldziej_2004,oldziej_2004_02}.
-The 4P and 1L2Y\_1LE1 force fields have considerable power independent of structural class.
+The 4P and E0LL2Y force fields have considerable power independent of structural class.
The ALPHA, BETA, and ALPHABETA force fields (for CSA) were used in the CASP4 exercises
and the CASP5 force field was used in the CASP5 exercise with some success; ALPHA
predicts reasonably the structure of $\alpha$-helical proteins and is still not obsolete,
\item{UNRES\_PBD} -- the starting/reference structure is read from an UNRES-generated
PDB file.
+\item{NSAXS} -- number of distance-distribution bins corresponding to to SAXS
+restraints (to be included in further section of the input).
+
+\item{SCAL\_RAD} -- scaling factor of sidechain radii in calculating Gaussian-smoothed distance distribution.
+
+\item{BOXX, BOXY, BOXZ} - periodic-box dimensions.
+
\end{description}
Keywords: PDBOUT, MOL2OUT, PDBREF, and PDBSTART are ignored for a CSA run.
\end{description}
-\subsubsection{Energy-term weights}
+\subsubsection{Energy-term and restraint weights}
\label{sect:input:main:weights}
(Data list format; subroutine MOLREAD.)
\item{WTOR=number} (real) (1.0d0) --
weight of the torsional term, $U_{tor}$.
+\item{WTORD=number} (real) (1.0d0) --
+weight of the double-torsional term, $U_{tord}$.
+
+\item{WSCCOR=number} (real) (1.0d0) --
+weight of the backbone-sidechain-torsional term, $U_{sccor}$.
+
\item{WANG=number} (real) (1.0d0) --
weight of the virtual-bond angle bending term, $U_b$.
\item{DELT\_CORR} (0.5) - thickness of the distance range in which the energy is
decreased to zero.
+\item{WSAXS=number} (real) (1.0d0) -- weight of the maximum-likelihood SAXS-restraint term.
+
\end{description}
The defaults are NOT the recommended values. No ``working'' default values
is the CA(i-2)-CA(i-1)-CA(i) virtual-bond angle and PHI(i) is the
CA(i-3)-CA(i-2)-CA(i-1)-CA(i) virtual-bond dihedral angle $\gamma$.
+
+\subsubsection{Distance-distribution (SAXS-restraint) data}
+
+This section contains the probability distribution ($P(r)$) from SAXS
+measurements to be used as restraints through introduction of a maximum-likelihood term.
+Each entry is in a separate like and the number of entries must equal to
+NSAXS specified in the first data record. Each line contains the position
+of the left side of the distance bin and probability-distribution value, for
+example:
+
+\begin{verbatim}
+0.7100E-00 0.2036E-03
+0.1420E+01 0.4221E-03
+\end{verbatim}
+
+The distance-distribution values do not need to be input in normalized form.
+Normalization is carried out automatically. It should be noted that neither
+probabilities nor distances can be zero; otherwise the calculations will crash.
+Therefore, entries with zeros must be eliminated from the data.
+
\subsubsection{Internal coordinates of the initial conformation}
\label{sect:input:main:intcoord}
projects / unres.git / blobdiff