Fri Oct 28 23:09:35 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Fri Oct 28 2011 at 23:09:35 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3827 !!! WARNING: LEU 36 has a net charge of 0.2480 !!! WARNING: NMA 58 has a net charge of 1.4000 !!! WARNING: HID 78 has a net charge of 1.4000 !!! WARNING: NMA 137 has a net charge of 1.4000 !!! WARNING: NMA 153 has a net charge of 1.4000 !!! WARNING: GLU 155 has a net charge of -0.7520 !!! WARNING: HIE 184 has a net charge of 1.4000 !!! WARNING: NMA 213 has a net charge of 1.4000 !!! WARNING: HIE 230 has a net charge of 1.4000 !!! WARNING: HIP 251 has a net charge of 1.4000 !!! WARNING: NMA 253 has a net charge of 1.4000 !!! WARNING: MET 255 has a net charge of 0.2480 !!! WARNING: NMA 274 has a net charge of 1.4000 !!! WARNING: HID 316 has a net charge of 2.8000 !!! WARNING: CYS 338 has a net charge of 0.2480 !!! WARNING: ARG 342 has a net charge of 1.2480 !!! WARNING: HID 353 has a net charge of 1.4000 !!! WARNING: HIP 368 has a net charge of 1.4000 !!! WARNING: NMA 374 has a net charge of 1.4000 !!! WARNING: PHE 376 has a net charge of 0.2480 !!! WARNING: HIP 396 has a net charge of 1.4000 !!! WARNING: NMA 398 has a net charge of 1.4000 !!! WARNING: GLU 400 has a net charge of -0.7520 !!! WARNING: ASN 403 has a net charge of 0.1680 !!! WARNING: HIP 411 has a net charge of 1.4000 !!! WARNING: CYM 435 has a net charge of 1.4000 !!! WARNING: NMA 453 has a net charge of 1.4000 !!! WARNING: LEU 458 has a net charge of 0.2480 !!! WARNING: NMA 485 has a net charge of 1.4000 !!! WARNING: PHE 487 has a net charge of 0.2480 !!! WARNING: HEM 500 has a net charge of 2.4000 !!! WARNING: WAT 600 has a net charge of 0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5351774 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -27.21000 39.31000 ymin,ymax (A): 1.452000 55.11700 zmin,zma (A): -33.48600 25.43300 x,y,z range (A): 66.52000 53.66500 58.91900 scale (grids/A): 0.5351774 object centre (A): 6.050001 28.28450 -4.026500 number of atom coordinates read : 3827 total number of charged atoms : 3465 net assigned charge : 32.03394 assigned positive charge : 559.9397 centred at (gu) : 89.66708 89.36235 91.58525 assigned negative charge : -527.9072 centred at (gu) : 89.73845 89.47513 91.62406 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6937 nv = 96 ne = 84 npr = 79151 no. pairs analyzed = 79151 no. exposed pairs = 4822 no. arc points = 33814 no. surface atoms = 1607 nbur = 2220 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 277 mr = 3556 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3645 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3177 ## 390 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8985 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0129835E-09 1.6022068E-09 midg,1,midg; midg,igrid,midg 2.1912188E-09 5.9803096E-10 1,midg,midg; igrid,midg,midg 1.8011910E-09 8.4487345E-10 gauss-seidel spectral radius is 0.9820715 estimated iterations to convergence 62 setup time was (sec) 0.4500000 now iterating at: 23:09:36 rms-change max change #iterations 9.2373319E-02 14.84421 at 10iterations 7.6901610E-03 1.286110 at 20iterations 1.2805178E-03 0.3052292 at 30iterations 2.9315130E-04 7.4066162E-02 at 40iterations 7.0600574E-05 1.7990112E-02 at 50iterations finished qdiffx linear iterations at : 23:09:39 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 7.0600574E-05 1.7990112E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 23:09:39 3.499u 0.208s 0:04.16 88.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Fri Oct 28 2011 at 23:09:39 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3827 !!! WARNING: LEU 36 has a net charge of 0.2480 !!! WARNING: NMA 58 has a net charge of 1.4000 !!! WARNING: HID 78 has a net charge of 1.4000 !!! WARNING: NMA 137 has a net charge of 1.4000 !!! WARNING: NMA 153 has a net charge of 1.4000 !!! WARNING: GLU 155 has a net charge of -0.7520 !!! WARNING: HIE 184 has a net charge of 1.4000 !!! WARNING: NMA 213 has a net charge of 1.4000 !!! WARNING: HIE 230 has a net charge of 1.4000 !!! WARNING: HIP 251 has a net charge of 1.4000 !!! WARNING: NMA 253 has a net charge of 1.4000 !!! WARNING: MET 255 has a net charge of 0.2480 !!! WARNING: NMA 274 has a net charge of 1.4000 !!! WARNING: HID 316 has a net charge of 2.8000 !!! WARNING: CYS 338 has a net charge of 0.2480 !!! WARNING: ARG 342 has a net charge of 1.2480 !!! WARNING: HID 353 has a net charge of 1.4000 !!! WARNING: HIP 368 has a net charge of 1.4000 !!! WARNING: NMA 374 has a net charge of 1.4000 !!! WARNING: PHE 376 has a net charge of 0.2480 !!! WARNING: HIP 396 has a net charge of 1.4000 !!! WARNING: NMA 398 has a net charge of 1.4000 !!! WARNING: GLU 400 has a net charge of -0.7520 !!! WARNING: ASN 403 has a net charge of 0.1680 !!! WARNING: HIP 411 has a net charge of 1.4000 !!! WARNING: CYM 435 has a net charge of 1.4000 !!! WARNING: NMA 453 has a net charge of 1.4000 !!! WARNING: LEU 458 has a net charge of 0.2480 !!! WARNING: NMA 485 has a net charge of 1.4000 !!! WARNING: PHE 487 has a net charge of 0.2480 !!! WARNING: HEM 500 has a net charge of 2.4000 !!! WARNING: WAT 600 has a net charge of 0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.605532 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -27.21000 39.31000 ymin,ymax (A): 1.452000 55.11700 zmin,zma (A): -33.48600 25.43300 x,y,z range (A): 66.52000 53.66500 58.91900 scale (grids/A): 1.605532 object centre (A): 6.050001 28.28450 -4.026500 number of atom coordinates read : 3827 total number of charged atoms : 3465 net assigned charge : 32.03394 assigned positive charge : 559.9397 centred at (gu) : 89.00019 88.08582 94.75478 assigned negative charge : -527.9072 centred at (gu) : 89.21478 88.42484 94.87188 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 77676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33814 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23770 mr = 52663 m= 2491 mr = 16304 m= 60 mr = 1256 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 589 time to turn everything in is 0.4000000 number of dielectric boundary points 33773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 26480 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5351774 object centre at (A) : 6.050001 28.28450 -4.026500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2504108E-02 3.5149783E-02 midg,1,midg; midg,igrid,midg 3.0581061E-02 1.5163555E-02 1,midg,midg; igrid,midg,midg 4.5002151E-02 2.1219160E-02 gauss-seidel spectral radius is 0.9982140 estimated iterations to convergence 188 setup time was (sec) 0.6300000 now iterating at: 23:09:40 rms-change max change #iterations 3.812990 184.1498 at 10iterations 1.594729 54.68486 at 20iterations 0.6683125 22.82968 at 30iterations 0.2814608 9.754246 at 40iterations 0.1190453 4.130760 at 50iterations 4.9973894E-02 1.894022 at 60iterations 2.1154592E-02 0.8079491 at 70iterations 9.0487348E-03 0.3147116 at 80iterations 3.9499048E-03 0.1252441 at 90iterations 1.7468769E-03 6.6184998E-02 at 100iterations 7.9971395E-04 3.4881592E-02 at 110iterations 3.8694934E-04 1.8386841E-02 at 120iterations finished qdiffx linear iterations at : 23:09:47 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 3.8694934E-04 1.8386841E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 23:09:48 7.912u 0.204s 0:08.48 95.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Fri Oct 28 2011 at 23:09:48 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3827 !!! WARNING: LEU 36 has a net charge of 0.2480 !!! WARNING: NMA 58 has a net charge of 1.4000 !!! WARNING: HID 78 has a net charge of 1.4000 !!! WARNING: NMA 137 has a net charge of 1.4000 !!! WARNING: NMA 153 has a net charge of 1.4000 !!! WARNING: GLU 155 has a net charge of -0.7520 !!! WARNING: HIE 184 has a net charge of 1.4000 !!! WARNING: NMA 213 has a net charge of 1.4000 !!! WARNING: HIE 230 has a net charge of 1.4000 !!! WARNING: HIP 251 has a net charge of 1.4000 !!! WARNING: NMA 253 has a net charge of 1.4000 !!! WARNING: MET 255 has a net charge of 0.2480 !!! WARNING: NMA 274 has a net charge of 1.4000 !!! WARNING: HID 316 has a net charge of 2.8000 !!! WARNING: CYS 338 has a net charge of 0.2480 !!! WARNING: ARG 342 has a net charge of 1.2480 !!! WARNING: HID 353 has a net charge of 1.4000 !!! WARNING: HIP 368 has a net charge of 1.4000 !!! WARNING: NMA 374 has a net charge of 1.4000 !!! WARNING: PHE 376 has a net charge of 0.2480 !!! WARNING: HIP 396 has a net charge of 1.4000 !!! WARNING: NMA 398 has a net charge of 1.4000 !!! WARNING: GLU 400 has a net charge of -0.7520 !!! WARNING: ASN 403 has a net charge of 0.1680 !!! WARNING: HIP 411 has a net charge of 1.4000 !!! WARNING: CYM 435 has a net charge of 1.4000 !!! WARNING: NMA 453 has a net charge of 1.4000 !!! WARNING: LEU 458 has a net charge of 0.2480 !!! WARNING: NMA 485 has a net charge of 1.4000 !!! WARNING: PHE 487 has a net charge of 0.2480 !!! WARNING: HEM 500 has a net charge of 2.4000 !!! WARNING: WAT 600 has a net charge of 0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.408298 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -27.21000 39.31000 ymin,ymax (A): 1.452000 55.11700 zmin,zma (A): -33.48600 25.43300 x,y,z range (A): 66.52000 53.66500 58.91900 scale (grids/A): 2.408298 object centre (A): 6.050001 28.28450 -4.026500 number of atom coordinates read : 3827 total number of charged atoms : 3465 net assigned charge : 32.03394 assigned positive charge : 559.9397 centred at (gu) : 88.50011 87.12855 97.13177 assigned negative charge : -527.9072 centred at (gu) : 88.82185 87.63709 97.30766 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 180892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33814 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 82549 mr = 129494 m= 23731 mr = 64723 m= 3819 mr = 18001 m= 242 mr = 2574 m= 0 mr = 107 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1941 time to turn everything in is 0.9400000 number of dielectric boundary points 76334 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 27679 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.605532 object centre at (A) : 6.050001 28.28450 -4.026500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2626028 0.4351755 midg,1,midg; midg,igrid,midg 0.4451073 0.2514173 1,midg,midg; igrid,midg,midg 0.7164339 0.2903592 gauss-seidel spectral radius is 0.9991695 estimated iterations to convergence 274 setup time was (sec) 1.170000 now iterating at: 23:09:49 rms-change max change #iterations 9.730591 513.3489 at 10iterations 5.508282 122.5340 at 20iterations 3.109455 69.41840 at 30iterations 1.741568 33.01717 at 40iterations 0.9743978 19.49144 at 50iterations 0.5457566 10.72453 at 60iterations 0.3050848 5.781326 at 70iterations 0.1699849 3.435402 at 80iterations 9.4598904E-02 1.861057 at 90iterations 5.2597340E-02 0.9415894 at 100iterations 2.9317727E-02 0.5859852 at 110iterations 1.6307203E-02 0.3025513 at 120iterations 9.1141174E-03 0.1793594 at 130iterations 5.0905785E-03 0.1015244 at 140iterations 2.8508441E-03 5.4725647E-02 at 150iterations 1.6010273E-03 3.1211853E-02 at 160iterations 9.0766780E-04 2.0107031E-02 at 170iterations 5.2199711E-04 1.2645721E-02 at 180iterations finished qdiffx linear iterations at : 23:10:01 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 5.2199711E-04 1.2645721E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 23:10:01 12.761u 0.249s 0:13.38 97.1% 0+0k 0+0io 0pf+0w