From: Cezary Czaplewski Date: Thu, 28 Mar 2019 13:52:18 +0000 (+0100) Subject: doc update X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=7dd2a0723a7ee82fbdde6aecb5cbbf488130becb doc update --- diff --git a/doc/3.2.1/latex/clusterman.pdf b/doc/3.2.1/latex/clusterman.pdf index 4387af9..62df6a5 100644 Binary files a/doc/3.2.1/latex/clusterman.pdf and b/doc/3.2.1/latex/clusterman.pdf differ diff --git a/doc/3.2.1/latex/clusterman.tex b/doc/3.2.1/latex/clusterman.tex index 65b38af..08755e3 100644 --- a/doc/3.2.1/latex/clusterman.tex +++ b/doc/3.2.1/latex/clusterman.tex @@ -353,6 +353,13 @@ Instead of IOPT=1, MINTREE and instead of IOPT=2 MINVAR can be specified \item{PUNCH\_DIST} -- if present, the upper-triangle of the distance matrix will be printed to a 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} \subsubsection{Energy-term weights and parameter files} @@ -398,6 +405,8 @@ Instead of IOPT=1, MINTREE and instead of IOPT=2 MINVAR can be specified \item{SCAL14} (0.4) -- scaling factor of 1,4-interactions +\item{WSAXS=number} (real) (1.0d0) -- weight of the maximum-likelihood SAXS-restraint term. + \end{description} \subsubsection{Molecule information} diff --git a/doc/3.2.1/latex/installman.pdf b/doc/3.2.1/latex/installman.pdf index 8e958f0..f4acf48 100644 Binary files a/doc/3.2.1/latex/installman.pdf and b/doc/3.2.1/latex/installman.pdf differ diff --git a/doc/3.2.1/latex/installman.tex b/doc/3.2.1/latex/installman.tex index 9e24906..b4d9a12 100644 --- a/doc/3.2.1/latex/installman.tex +++ b/doc/3.2.1/latex/installman.tex @@ -301,14 +301,26 @@ is also specified for the CSA and MINIM component. \section{TECHNICAL SUPPORT CONTACT INFORMATION} \label{sect:support} - Dawid Jagie{\l}a\\ + Cezary Czaplewski\\ Faculty of Chemistry, University of Gdansk\\ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\ - fax: +48 58 523 5012\\ - e-mail: \href{mailto:lightnir@gmail.com}{lightnir@gmail.com}\\ + fax: +48 58 523 5128\\ + e-mail: \href{mailto:cezary.czaplewski@ug.edu.pl}{cezary.czaplewski@ug.edu.pl}\\ + + Adam K. Sieradzan\\ + Faculty of Chemistry, University of Gdansk\\ + ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\ + fax: +48 58 523 5128\\ + e-mail: \href{mailto:adams86@wp.pl}{adams86@wp.pl}\\ + + Adam Liwo\\ + Faculty of Chemistry, University of Gdansk\\ + ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\ + fax: +48 58 523 5124\\ + e-mail: \href{mailto:adam.liwo@ug.edu.pl}{adam.liwo@ug.edu.pl}\\ \small{ - Prepared by Dawid Jagie{\l}a and Adam Liwo, 4/12/2014\\ + Prepared by Dawid Jagie{\l}a and Adam Liwo, 4/12/2014, updated 12/21/2018\\ } \end{document} diff --git a/doc/3.2.1/latex/unresman.pdf b/doc/3.2.1/latex/unresman.pdf index c67bc1c..cbcb767 100644 Binary files a/doc/3.2.1/latex/unresman.pdf and b/doc/3.2.1/latex/unresman.pdf differ diff --git a/doc/3.2.1/latex/unresman.tex b/doc/3.2.1/latex/unresman.tex index 6ec0dc5..bf3de70 100644 --- a/doc/3.2.1/latex/unresman.tex +++ b/doc/3.2.1/latex/unresman.tex @@ -457,6 +457,32 @@ Revised backbone-virtual-bond-angle potentials to treat the L- and D-amino 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 @@ -1112,6 +1138,13 @@ See refs. \cite{liwo_1997_02} and \cite{liwo_1997_03}. \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. @@ -1663,7 +1696,7 @@ single run but only temperature exchange. \end{description} -\subsubsection{Energy-term weights} +\subsubsection{Energy-term and restraint weights} \label{sect:input:main:weights} (Data list format; subroutine MOLREAD.) @@ -1712,6 +1745,12 @@ segment, 6rd order contributions). \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, $U_b$. @@ -1734,6 +1773,8 @@ and higher-order correlations. \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 @@ -2106,6 +2147,26 @@ ALPHA(i) and OMEG(i) correspond to the side chain attached to CA(i). THETA(i) 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} diff --git a/doc/3.2.1/latex/whamman.pdf b/doc/3.2.1/latex/whamman.pdf index 9f42835..e2b4252 100644 Binary files a/doc/3.2.1/latex/whamman.pdf and b/doc/3.2.1/latex/whamman.pdf differ diff --git a/doc/3.2.1/latex/whamman.tex b/doc/3.2.1/latex/whamman.tex index 3d7670a..1816fdb 100644 --- a/doc/3.2.1/latex/whamman.tex +++ b/doc/3.2.1/latex/whamman.tex @@ -264,6 +264,12 @@ ref \cite{oldziej_2004}. \item{RESCALE} (1) -- Choice of the type of temperature dependence of the force field. +\item{NSAXS} -- number of distance-distribution bins corresponding to to SAXS + +\item{SCAL\_RAD} -- scaling factor of sidechain radii in calculating Gaussian-smoothed distance distribution. + +\item{BOXX, BOXY, BOXZ} - periodic-box dimensions. + \begin{description} \item{$>0$} -- no temperature dependence. @@ -388,6 +394,7 @@ All items described in this section are input in keyword-based mode. \item{WSCCOR} (1.0) -- sequence-specific virtual-bond-torsional energy. \item{WDIHC} (0.0) -- dihedral-angle-restraint energy. \item{WHPB} (1.0) -- distance-restraint energy. +\item{WSAXS=number} (real) (1.0d0) -- weight of the maximum-likelihood SAXS-restraint term. \end{description}