Xplor-NIH version 2.25 C.D. Schwieters, J.J. Kuszewski, Progr. NMR Spectr. 48, 47-62 (2006). N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih based on X-PLOR 3.851 by A.T. Brunger User: noi on: duo-suse (x86/Linux ) at: 29-Feb-12 15:09:18 [stdin](1): execfile('buildpsf.py') buildpsf.py(6): xplor.requireVersion("2.12") buildpsf.py(8): xplor.parseArguments() # check for typos on the command-line buildpsf.py(28): """ buildpsf.py(30): simWorld.setRandomSeed(5521) buildpsf.py(32): import protocol buildpsf.py(33): protocol.initTopology(('protein','cyc_impr_bridge_flex.top')) X-PLOR>rtf @TOPPAR:protein.top end ASSFIL: file /home/noi/bin/xplor-nih-2.25/toppar/protein.top opened. RTFRDR>! RTFRDR>! xplor-nih protein topology file, version 1.0 RTFRDR>! RTFRDR>! This file is intended to work with the parameter file protein-1.0.par RTFRDR>! RTFRDR>! This is a re-named copy of the file topallhdg_new.pro RTFRDR>! RTFRDR>! We've created this new filename in order to eliminate confusion RTFRDR>! between the various parameter/topology combinations that ship RTFRDR>! with xplor-nih. It has version numbers, and will be updated RTFRDR>! along with the rest of the xplor-nih package. RTFRDR>! RTFRDR>! Its backbone bond lengths and angles are designed to agree with RTFRDR>! the Engh & Huber parameter set (reference below), which is used by RTFRDR>! PROCHECK, among other structure-validation programs. RTFRDR>! RTFRDR>! If you find errors, PLEASE let us know. RTFRDR>! RTFRDR> RTFRDR>remark file protein-1.0.top RTFRDR>remark geometric energy function topology for distance geometry and RTFRDR>remark simulated annealing. RTFRDR>remark RTFRDR>remark history: RTFRDR>remark RTFRDR>remark XPLOR topology file TOPALLHSA.PRO, all hydrogens, RTFRDR>remark for simulated annealing, to be used with PARALLHSA.PRO RTFRDR>remark based on TOPALLH6.PRO. RTFRDR>remark internal coordinates from TOPH19.PRO. RTFRDR>remark doubly protonated histidine. RTFRDR>! all dihedrals defining planarity have been converted to impropers, RTFRDR>! the only dihedrals left are around rotatable bonds. RTFRDR>! some additional impropers were included in the rings to define planarity RTFRDR>! better. patches are included to define chirality at stereospecifically RTFRDR>! assigned prochiral centres and convert from trans to cis peptide bond. RTFRDR>! modifications by M. Nilges and P. Kraulis. RTFRDR>! added stereospecific impropers for all pro-chiral centers (ATB) RTFRDR> RTFRDR>! RTFRDR>remark corrected proline angles to Engh & Huber, Acta Cryst., A47, 392 (1991) values. RTFRDR>remark Needed to define a new atom type, CP, which is equivalent to their RTFRDR>remark CH2P atom type. JJK 9/22/95 RTFRDR>! RTFRDR> RTFRDR>set message off echo off end RTFRDR> end X-PLOR>end X-PLOR>rtf @cyc_impr_bridge_flex.top end ASSFIL: file /home/noi/work/nmr/pixj/dipo/ipapfhsqc/diff/cyc_impr_bridge_flex.top opened. RTFRDR>Remarks drg.top RTFRDR>Remarks Created by XPLO2D V. 050802/3.3.2 at Fri Mar 13 19:26:02 2009 for noi RTFRDR>Remarks Auto-generated by XPLO2D from file cyc.pdb_orig RTFRDR>Remarks You *MUST* check/edit MASSes and CHARges !!! RTFRDR>Remarks Check DONOrs and ACCEptors RTFRDR>Remarks Verify IMPRopers yourself RTFRDR>Remarks DIHEdrals which are not flat are commented out RTFRDR> RTFRDR> set echo=false end buildpsf.py(34): protocol.initParams(('protein','cyc_impr_bridge_flex.par')) ASSFIL: file /home/noi/bin/xplor-nih-2.25/toppar/protein.par opened. ASSFIL: file /home/noi/work/nmr/pixj/dipo/ipapfhsqc/diff/cyc_impr_bridge_flex.par opened. PARRDR> PARRDR> end X-PLOR>end buildpsf.py(36): import psfGen buildpsf.py(37): psfGen.seqToPSF(seq,seqType='prot',startResid=1) buildpsf.py(39): from pdbTool import PDBTool buildpsf.py(40): PDBTool('xray.pdb').read() PDBTool:read: atom not found in structure: LEU 165 O PDBTool:read: atom not found in structure: HIS 166 O PDBTool:read: atom not found in structure: HIS 166 N PDBTool:read: atom not found in structure: HIS 166 CA PDBTool:read: atom not found in structure: HIS 166 C PDBTool:read: atom not found in structure: HIS 166 CB PDBTool:read: atom not found in structure: HIS 166 CG PDBTool:read: atom not found in structure: HIS 166 ND1 PDBTool:read: atom not found in structure: HIS 166 CD2 PDBTool:read: atom not found in structure: HIS 166 CE1 PDBTool:read: atom not found in structure: HIS 166 NE2 PDBTool:read: atom not found in structure: HIS 167 O PDBTool:read: atom not found in structure: HIS 167 N PDBTool:read: atom not found in structure: HIS 167 CA PDBTool:read: atom not found in structure: HIS 167 C PDBTool:read: atom not found in structure: HIS 167 CB PDBTool:read: atom not found in structure: HIS 167 CG PDBTool:read: atom not found in structure: HIS 167 ND1 PDBTool:read: atom not found in structure: HIS 167 CD2 PDBTool:read: atom not found in structure: HIS 167 CE1 PDBTool:read: atom not found in structure: HIS 167 NE2 PDBTool:read: atom not found in structure: HIS 168 O PDBTool:read: atom not found in structure: ð,„ HIS 168 N PDBTool:read: atom not found in structure: HIS 168 CA PDBTool:read: atom not found in structure: HIS 168 C PDBTool:read: atom not found in structure: HIS 168 CB PDBTool:read: atom not found in structure: HIS 168 CG PDBTool:read: atom not found in structure: HIS 168 ND1 PDBTool:read: atom not found in structure: HIS 168 CD2 PDBTool:read: atom not found in structure: HIS 168 CE1 PDBTool:read: atom not found in structure: HIS 168 NE2 PDBTool:read: atom not found in structure: HIS 169 O PDBTool:read: atom not found in structure: HIS 169 N PDBTool:read: atom not found in structure: HIS 169 CA PDBTool:read: atom not found in structure: HIS 169 C PDBTool:read: atom not found in structure: HIS 169 CB PDBTool:read: atom not found in structure: HIS 169 CG PDBTool:read: atom not found in structure: HIS 169 ND1 PDBTool:read: atom not found in structure: HIS 169 CD2 PDBTool:read: atom not found in structure: HIS 169 CE1 PDBTool:read: atom not found in structure: HIS 169 NE2 PDBTool:read: atom not found in structure: HIS 170 O PDBTool:read: atom not found in structure: HIS 170 N PDBTool:read: atom not found in structure: HIS 170 CA PDBTool:read: atom not found in structure: ð,„ HIS 170 C PDBTool:read: atom not found in structure: HIS 170 CB PDBTool:read: atom not found in structure: HIS 170 CG PDBTool:read: atom not found in structure: HIS 170 ND1 PDBTool:read: atom not found in structure: HIS 170 CD2 PDBTool:read: atom not found in structure: HIS 170 CE1 PDBTool:read: atom not found in structure: HIS 170 NE2 buildpsf.py(42): protocol.addUnknownAtoms(dyn_stepsize=0.01) buildpsf.py(45): PDBTool("xray_h.pdbn").write() HEAP: maximum use= 6116848 current use= 3042601 X-PLOR: total CPU time= 377.7200 s X-PLOR: entry time at 15:09:18 29-Feb-12 X-PLOR: exit time at 15:15:37 29-Feb-12