From: Adam Liwo Date: Fri, 12 Dec 2014 00:43:11 +0000 (+0100) Subject: Documentation updated X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=cac632b968ece398a6176960617c770d9afd3f71 Documentation updated --- diff --git a/doc/3.2.1/latex/installman.pdf b/doc/3.2.1/latex/installman.pdf index 46d17ef..8e958f0 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 265d7d0..9e24906 100644 --- a/doc/3.2.1/latex/installman.tex +++ b/doc/3.2.1/latex/installman.tex @@ -240,7 +240,8 @@ If option 1 fails or your MPI implementation does not come with a compiler wrapp \section{Step-by-step installation} \label{sect:stepbystep} -For this installation, you will need to visit each source directory (see doc/UNRESPACK.txt +For this installation, you will need to visit each source directory (see +Figure \ref{fig:distr} for directory structure). Specific installation instructions are in the documentation of of the particular components of the package (UNRES, WHAM, CLUSTER, XDRFPDB). Only general instructions are given here. diff --git a/doc/3.2.1/latex/unresman.pdf b/doc/3.2.1/latex/unresman.pdf index 5bf0e0d..c67bc1c 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 caaa183..6ec0dc5 100644 --- a/doc/3.2.1/latex/unresman.tex +++ b/doc/3.2.1/latex/unresman.tex @@ -958,13 +958,13 @@ to generate random conformations: 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,