X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=examples%2Funres%2FCSA%2FEXAMPLES.TXT;fp=examples%2Funres%2FCSA%2FEXAMPLES.TXT;h=0000000000000000000000000000000000000000;hp=e52beb2fade30cc627550c309bc968daa914ea9b;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/examples/unres/CSA/EXAMPLES.TXT b/examples/unres/CSA/EXAMPLES.TXT deleted file mode 100644 index e52beb2..0000000 --- a/examples/unres/CSA/EXAMPLES.TXT +++ /dev/null @@ -1,237 +0,0 @@ -* This software is provided free of charge to academic users, subject to the - condition that no part of it be sold or used otherwise for commercial - purposes, including, but not limited to its incorporation into commercial - software packages, without written consent from the authors. For permission - contact Prof. H. A. Scheraga, Cornell University. - -* This software package is provided on an "as is" basis. We in no way warrant - either this software or results it may produce. - -* Reports or publications using this software package must contain an - acknowledgement to the authors and the NIH Resource in the form commonly used - in academic research. - - DESCRIPTION OF UNRES/CSA EXAMPLES - - -1. General notes ----------------- - -The input and output files pertaining to the variations of the UNRES force field -described in UNRES.TXT are in the directory examples and subdirectories CASP3, ALPHA, -BETA, ALPHABETA, CASP5, 3P, and 4P, respectively. Each of these directories -contains subdirectory ENERGY and CSA; these contain examples of single-point -energy evaluation and minimization and CSA search, respectively. Both ENERGY -and CSA directories contain output subdirectories with sample output files; input -and script files are on the root level. Additionally, CASP5/CSA and ALPHABETA/CSA are -further divided into subdirectories pertaining to specific systems. - -The examples contained in ENERGY must be run to test a variation of the force field. -Check the energies obtained in output/*.out_GB000 (BEFORE minimzation) with your -results. Differences in any component larger than the last significant digit mean -that there is an error in your settings or installation. (Note that the differences -in energies AFTER minimization might be greater and are not a reason to worry.) -Check carefully the parameter files, in the C-shell script, the energy-term weights -in the *.inp file and the compiler flags specified in section 4. of UNRES.TXT. If -the differences persist, report the problem to the authors (contact information is -at the end of this file and UNRES.TXT. The energies (before and after minimization) -are listed in the title lines of the input files. - -The CSA results are stochastic and you might happen to get completely different -results than those contained in the output directories. Apart from (perhaps) -ALPHA and 4P the other force fields exhibit some "glassy" behavior with the CSA -search method and the search happens to be trapped in higher-energy regions. -For each example, we have provided the lowest energy reached so far for that system, -if different from that in the example. We also provided the respective native -structure. - -To save space, in all cases except CASP5 only the master output file is provided. -See section 3. of UNRES.TXT for the description of the output files. - -The C-shell scripts for single-point energy evaluation are for interactive runs, -while those for CSA calculations are for batch runs. In each case the master batch -script is start.mat. The batch scripts are for the PBS system. - -2. Single-point energy evaluation and minimization tests --------------------------------------------------------- - -CASP3 - -The input file protA.inp and the pertinent output files in output contain the data -and results of energy evaluation and subsequent minimization of the NMR structure -of the 46-residue fragment of the B-domain of staphylococcal protein A. The -C-shell script file is unres_casp3.csh. - -The input file proteinA_rms.inp and the pertinent output files contain the data and -results of energy evaluation and minimization and the evaluation of the RMSD from the -NMR structure (prota_nmr.pdb) for a native-like conformation obtained in CSA -search; this structure is native-like [1]. - -ALPHA - -The input file T0102.inp and the pertinent output files contain the data and results -of energy evaluation and minimization of the lowest-energy structure of bacteriocin -As-48 (CASP4 target T0102; PDB code: 1E68) obtained in the CASP4 exercise [2]. The -structure is native-like. - -BETA - -The input file T0105.inp and the pertinent output files contain the data and results -of energy evaluation and minimization of the lowest-energy structure of the human -Sp100B sand domain (CASP4 target T0105; PDB code: 1H5P). This middle beta-hairpin -corresponds to the hairpin in the native structure. - -ALPHABETA - -The input file T0104.inp and the pertinent output files contain the data and results -of energy evaluation and minimization of the lowest-energy conformation of Yjee -protein (CASP4 target T0104; PDB code: 1FL9). The structure has some similarity to -the native structure in the N-terminal part. - -CASP5 - -The input file 1igd.inp and the pertinent output files contain the data and results -of energy calculation and minimization for for the lowest-energy structure of the -IGG domain (1IGD). The structure is native-like except misalignment of the two -beta-hairpins. The C-shell script is unres_casp5_1igd.csh. - -The input file t0132.inp and the pertinent output files contain the data and results -of energy calculation and minimization for the lowest-energy conformation of -HI0827 (CASP5 target: T0132). The structure shares some features with the native -structures; the latter has not been published yet. The C-shell script is -unres_casp5_t0149c.csh. - -The input file T0149C_dihc.inp and the pertinent output files contain the data and -results of energy calculation and minimization for the lowest-energy conformation of -the C-terminal domain of the Yjia protein (CASP5 target: T0149; PDB code: 1NIJ). -The structure shares and about 80-residue segment with the native structure. -The C-shell script is unres_casp5_t0149c.csh. Dihedral-angle restraints from -secondary-structure prediction were used; they are included in T0149C_dihc.spred. - -3P - -The file IGD_3P7_iter81_1_i1.inp and the pertinent output files contain the results -of energy evaluation and minimization of the lowest-enerrgy conformation of 1IGD. -The structure shares the topology with the native structure, but the RMSD is -6.3 A. - -4P - -The file 4P5_iter33_3_i3.inp and the pertinent output files contain the results -of energy evaluation and minimization of the lowest-enerrgy conformation of 1IGD. -The structure shares the topology with the native structure, but the RMSD is about -5.6 A. - -3. CSA calculations -------------------- - -CASP3 - -The example pertains to protein A. The search resulted in the mirror image of -the native structure (which is not the lowest-energy structure; the lowest energy -ever found is -157.103 kcal/mol and corresponds to a native-like structure). -Native-like structures are, however, present in the final bank. The files -proteinA_CASP3@???.pdb contain the lowest-energy conformations found by CSA every -100 minimizations; they can be used to construct the "evolution path" of the -system. The experimental structure is in prota_nmr.pdb. - -ALPHA - -The example also pertains to protein A. The search results in a native-like -structure as the lowest-energy structure with RMSD=3.2 A from the NMR structure. -The experimental structure is in prota_nmr.pdb. - -BETA - -The example pertains to the betanova three-stranded beta-sheet peptide. The native- -like structure is obtained in the search. The experimental structure is in -bh35.pdb (it should be noted that this structure was not accepted by the PDB and -the only certain information from the experiment is that this peptide forms -predominantly a three-stranded beta-sheet). - -ALPHABETA - -The CSA directory is divided into the BETANOVA and proteinA subdirectories for -these two molecules. In both cases the search results in a native-like structure -as the lowest-energy structure. - -CASP5 - -The example pertains to the 1FSD alpha/beta peptide. The directory run1 corresponds -to a "successful" run in which a native-like alpha/beta structure was obtained, while -the directory run2 to an "unsuccesful" one, in which a three-stranded non-native -beta-sheet was obtained as the lowest-energy structure. However, even this -native-like structure has a higher energy than the lowest energy structure found -so far (-77.518 kcal/mol; native-like). The NMR structure is in 1FSD.pdb. - -3P - -The example pertains to 1IGD. This run has led to a non-native "negative" of -the protein, in which the beta-sheet is formed in the middle of the sequence and -not in the N- and the C-end. The energy is much higher than that of the lowest-energy -native structure, which is -745.355 kcal/mol. The native structure is in 1igd.pdb. - -4P - -Another 1IGD example; this time the search resulted in the native structure. -However, the energy is higher than the lowest energy found (-747.433 kcal/mol). - - -4. References -------------- - -[1] J. Lee, A. Liwo, H.A. Scheraga. Conformational space annealing and an - off-lattice united-residue force field: application to the 10-55 fragment of - staphylococcal protein A and to apo calbindin D9K. Proc. Natl. Acad. Sci. USA}, - 1999, 96, 2025-2030. - -[2] J. Pillardy, C. Czaplewski, A. Liwo, J. Lee, D.R. Ripoll, R. Kazmierkiewicz, - St. Oldziej, W.J. Wedemeyer, K.D. Gibson, Y.A. Arnautova, J. Saunders, - Y.-J. Ye, H. A. Scheraga. Recent improvements in prediction of protein structure - by global optimization of a potential energy function. Proc. Natl. Acad. Sci. - USA, 2001, 98, 2329--2333. - - - -5. Contact information ----------------------- - - Dr. Adam Liwo - Faculty of Chemistry, University of Gdansk - ul. Sobieskiego 18, 80-952 Gdansk Poland. - phone: +48 58 345 0361 - fax: +48 58 341 0357 - e-mail: adam@chem.univ.gda.pl - - Dr. Cezary Czaplewski - Faculty of Chemistry, University of Gdansk - ul. Sobieskiego 18, 80-952 Gdansk Poland. - phone: +48 58 345 0361 - fax: +48 58 341 0357 - e-mail: czarek@chem.univ.gda.pl - - Dr. Stanislaw Oldziej - Baker Laboratory of Chemistry and Chemical Biology - Cornell University - Ithaca, NY 14853-1301, U.S.A. - phone: (607) 255 0556 - fax: (607) 255 4137 - e-mail: stan@scheraga2.chem.cornell.edu - - Dr. Jaroslaw Pillardy - Baker Laboratory of Chemistry and Chemical Biology - Cornell University - Ithaca, NY 14853-1301, U.S.A. - phone: (607) 255 0556 - fax: (607) 255 4137 - e-mail: jp86@cornell.edu - - Dr. Jooyoung Lee - Korea Institute for Advanced Study - 207-43 Cheongryangri-dong Dongdaemun-gu - Seoul 130-012, Korea - phone: 82-2-958-3731 - fax: 82-2-958-3786 - e-mail: jlee@kias.re.kr - -Prepared by Adam Liwo, Cezary Czaplewski, and Stanislaw Oldziej, 9/1/03