Tue Oct 11 03:17:46 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+sph.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 = amb.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 Tue Oct 11 2011 at 03:17:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3416 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5785514 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): -11.31100 43.93900 ymin,ymax (A): 14.40600 75.11300 zmin,zma (A): 39.97500 101.5080 x,y,z range (A): 55.25000 60.70700 61.53300 scale (grids/A): 0.5785514 object centre (A): 16.31400 44.75950 70.74150 number of atom coordinates read : 3416 total number of charged atoms : 3277 net assigned charge : -7.043968 assigned positive charge : 514.9784 centred at (gu) : 88.37315 87.76569 88.43514 assigned negative charge : -522.0237 centred at (gu) : 88.40538 87.76606 88.43587 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7390 nv = 96 ne = 84 npr = 70056 no. pairs analyzed = 70056 no. exposed pairs = 4422 no. arc points = 30715 no. surface atoms = 1482 nbur = 1934 mkacc time = 0.1200000 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 = 1.484000 m= 361 mr = 3820 m= 2 mr = 20 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 3913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3164 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9513 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0654396E-09 -1.0392923E-09 midg,1,midg; midg,igrid,midg -2.4279434E-09 -8.9035662E-10 1,midg,midg; igrid,midg,midg -9.6486119E-10 -1.5486291E-09 gauss-seidel spectral radius is 0.9846140 estimated iterations to convergence 66 setup time was (sec) 0.4600000 now iterating at: 03:17:47 rms-change max change #iterations 0.1052958 16.84782 at 10iterations 8.3979703E-03 1.259781 at 20iterations 7.3268695E-04 9.3772888E-02 at 30iterations 1.2260933E-04 1.7416477E-02 at 40iterations 3.5610712E-05 6.0915947E-03 at 50iterations finished qdiffx linear iterations at : 03:17:50 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 3.5610712E-05 6.0915947E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 03:17:50 3.481u 0.159s 0:03.94 92.1% 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 Tue Oct 11 2011 at 03:17:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3416 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.735654 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): -11.31100 43.93900 ymin,ymax (A): 14.40600 75.11300 zmin,zma (A): 39.97500 101.5080 x,y,z range (A): 55.25000 60.70700 61.53300 scale (grids/A): 1.735654 object centre (A): 16.31400 44.75950 70.74150 number of atom coordinates read : 3416 total number of charged atoms : 3277 net assigned charge : -7.043968 assigned positive charge : 514.9784 centred at (gu) : 85.11832 83.29606 85.30462 assigned negative charge : -522.0237 centred at (gu) : 85.21548 83.29750 85.30724 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79624 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30715 grid for indexing accessible points = 1.400000 m= 28149 mr = 53233 m= 3764 mr = 20144 m= 141 mr = 1962 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 36324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 239 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 25358 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) : 0.5785514 object centre at (A) : 16.31400 44.75950 70.74150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8358093E-02 2.0181995E-02 midg,1,midg; midg,igrid,midg -2.8951978E-03 3.0997451E-03 1,midg,midg; igrid,midg,midg -3.0167170E-03 9.1291056E-04 gauss-seidel spectral radius is 0.9984363 estimated iterations to convergence 201 setup time was (sec) 0.6300000 now iterating at: 03:17:51 rms-change max change #iterations 4.102424 168.4344 at 10iterations 1.812882 59.29640 at 20iterations 0.8048813 30.35948 at 30iterations 0.3559340 11.27663 at 40iterations 0.1581183 5.366089 at 50iterations 7.0138052E-02 2.251933 at 60iterations 3.1151434E-02 0.9407768 at 70iterations 1.3874702E-02 0.4506130 at 80iterations 6.1684307E-03 0.2150409 at 90iterations 2.7819427E-03 9.1824532E-02 at 100iterations 1.2601989E-03 4.1603088E-02 at 110iterations 5.8778975E-04 1.7932415E-02 at 120iterations finished qdiffx linear iterations at : 03:17:58 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 5.8778975E-04 1.7932415E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 03:17:59 7.992u 0.199s 0:08.49 96.3% 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 Tue Oct 11 2011 at 03:17:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3416 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.603481 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): -11.31100 43.93900 ymin,ymax (A): 14.40600 75.11300 zmin,zma (A): 39.97500 101.5080 x,y,z range (A): 55.25000 60.70700 61.53300 scale (grids/A): 2.603481 object centre (A): 16.31400 44.75950 70.74150 number of atom coordinates read : 3416 total number of charged atoms : 3277 net assigned charge : -7.043968 assigned positive charge : 514.9784 centred at (gu) : 82.67739 79.94385 82.95666 assigned negative charge : -522.0237 centred at (gu) : 82.82310 79.94617 82.96079 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184113 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30715 grid for indexing accessible points = 1.400000 m= 91712 mr = 130078 m= 31885 mr = 73357 m= 6351 mr = 24784 m= 610 mr = 4182 m= 26 mr = 263 m= 0 mr = 3 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.000000 number of dielectric boundary points 82030 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 26200 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) : 1.735654 object centre at (A) : 16.31400 44.75950 70.74150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4064303 0.3954766 midg,1,midg; midg,igrid,midg 5.6961875E-02 0.3002475 1,midg,midg; igrid,midg,midg 4.4728690E-03 -1.7048314E-02 gauss-seidel spectral radius is 0.9992267 estimated iterations to convergence 284 setup time was (sec) 1.250000 now iterating at: 03:18:00 rms-change max change #iterations 10.32715 304.0533 at 10iterations 6.053184 133.0650 at 20iterations 3.495456 70.95323 at 30iterations 2.017822 45.07037 at 40iterations 1.159471 25.01729 at 50iterations 0.6652070 14.65697 at 60iterations 0.3802887 8.087860 at 70iterations 0.2170995 4.476371 at 80iterations 0.1237688 2.652287 at 90iterations 7.0651487E-02 1.446913 at 100iterations 4.0142704E-02 0.7515993 at 110iterations 2.2853000E-02 0.4199238 at 120iterations 1.2995923E-02 0.2277045 at 130iterations 7.3744976E-03 0.1397427 at 140iterations 4.1944785E-03 7.6321602E-02 at 150iterations 2.3873334E-03 4.7805786E-02 at 160iterations 1.3575043E-03 2.6941299E-02 at 170iterations 7.7609380E-04 1.4721870E-02 at 180iterations finished qdiffx linear iterations at : 03:18:12 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 7.7609380E-04 1.4721870E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 03:18:12 12.873u 0.217s 0:13.39 97.6% 0+0k 0+0io 0pf+0w