Sun Oct 9 06:04:57 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 Sun Oct 9 2011 at 06:04:58 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1728 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIR 136 has a net charge of 0.5140 !!! WARNING: ZN4 490 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7381297 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): -51.99600 -3.766000 ymin,ymax (A): 3.052000 47.84600 zmin,zma (A): 42.25300 87.01000 x,y,z range (A): 48.23000 44.79400 44.75700 scale (grids/A): 0.7381297 object centre (A): -27.88100 25.44900 64.63150 number of atom coordinates read : 1728 total number of charged atoms : 1584 net assigned charge : -5.979988 assigned positive charge : 264.6492 centred at (gu) : 89.28430 90.98549 89.57108 assigned negative charge : -270.6292 centred at (gu) : 89.44489 90.96088 90.00020 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6528 nv = 96 ne = 84 npr = 35264 no. pairs analyzed = 35264 no. exposed pairs = 2316 no. arc points = 16433 no. surface atoms = 788 nbur = 940 mkacc time = 5.9999995E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 3530 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.1400000 number of dielectric boundary points 3388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1316 ## 97 charges are in solution ## iepsmp to db, and charging done at 0.2100000 number of grid points assigned charge 6800 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5814987E-07 -4.3574150E-07 midg,1,midg; midg,igrid,midg -1.0324294E-07 -9.8792881E-08 1,midg,midg; igrid,midg,midg 3.2607304E-08 -2.0810432E-07 gauss-seidel spectral radius is 0.9903998 estimated iterations to convergence 83 setup time was (sec) 0.3300000 now iterating at: 06:04:58 rms-change max change #iterations 0.2341996 40.46062 at 10iterations 3.0865695E-02 4.766178 at 20iterations 4.1184342E-03 0.5593948 at 30iterations 5.5686262E-04 7.7495575E-02 at 40iterations 7.4773561E-05 1.0470390E-02 at 50iterations finished qdiffx linear iterations at : 06:05:01 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 7.4773561E-05 1.0470390E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:05:01 3.359u 0.194s 0:03.81 92.9% 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 Sun Oct 9 2011 at 06:05:01 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1728 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIR 136 has a net charge of 0.5140 !!! WARNING: ZN4 490 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.214389 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): -51.99600 -3.766000 ymin,ymax (A): 3.052000 47.84600 zmin,zma (A): 42.25300 87.01000 x,y,z range (A): 48.23000 44.79400 44.75700 scale (grids/A): 2.214389 object centre (A): -27.88100 25.44900 64.63150 number of atom coordinates read : 1728 total number of charged atoms : 1584 net assigned charge : -5.979988 assigned positive charge : 264.6492 centred at (gu) : 87.85318 92.95650 88.71326 assigned negative charge : -270.6292 centred at (gu) : 88.33486 92.88287 90.00095 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 67993 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16433 grid for indexing accessible points = 1.400000 m= 27325 mr = 45736 m= 5899 mr = 20581 m= 596 mr = 4013 m= 16 mr = 292 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 465 time to turn everything in is 0.3400000 number of dielectric boundary points 31205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 12607 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) : 0.7381297 object centre at (A) : -27.88100 25.44900 64.63150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9246457E-02 -0.1182459 midg,1,midg; midg,igrid,midg -6.5761872E-02 -7.0454866E-02 1,midg,midg; igrid,midg,midg 6.0377814E-02 -7.0117287E-02 gauss-seidel spectral radius is 0.9988872 estimated iterations to convergence 237 setup time was (sec) 0.5400000 now iterating at: 06:05:02 rms-change max change #iterations 4.750134 194.9268 at 10iterations 2.395345 90.67213 at 20iterations 1.204571 41.42037 at 30iterations 0.6058739 20.59839 at 40iterations 0.3060171 9.892225 at 50iterations 0.1544445 4.397333 at 60iterations 7.8063749E-02 2.261013 at 70iterations 3.9307121E-02 1.270592 at 80iterations 1.9844491E-02 0.5805206 at 90iterations 1.0010485E-02 0.3016033 at 100iterations 5.0479397E-03 0.1537714 at 110iterations 2.5491947E-03 7.6631546E-02 at 120iterations finished qdiffx linear iterations at : 06:05:09 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 2.5491947E-03 7.6631546E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 06:05:09 7.612u 0.221s 0:08.13 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 Sun Oct 9 2011 at 06:05:10 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1728 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIR 136 has a net charge of 0.5140 !!! WARNING: ZN4 490 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.321584 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): -51.99600 -3.766000 ymin,ymax (A): 3.052000 47.84600 zmin,zma (A): 42.25300 87.01000 x,y,z range (A): 48.23000 44.79400 44.75700 scale (grids/A): 3.321584 object centre (A): -27.88100 25.44900 64.63150 number of atom coordinates read : 1728 total number of charged atoms : 1584 net assigned charge : -5.979988 assigned positive charge : 264.6492 centred at (gu) : 86.77981 94.43481 88.06994 assigned negative charge : -270.6292 centred at (gu) : 87.50234 94.32441 90.00150 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 156302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16433 grid for indexing accessible points = 1.400000 m= 82654 mr = 110139 m= 35990 mr = 68088 m= 11307 mr = 29689 m= 2414 mr = 8839 m= 302 mr = 1774 m= 8 mr = 203 m= 0 mr = 3 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1699 time to turn everything in is 1.070000 number of dielectric boundary points 70242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 12672 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) : 2.214389 object centre at (A) : -27.88100 25.44900 64.63150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2348548E-02 -1.207421 midg,1,midg; midg,igrid,midg -0.4170006 -0.5764961 1,midg,midg; igrid,midg,midg 0.2117674 -1.184494 gauss-seidel spectral radius is 0.9993072 estimated iterations to convergence 300 setup time was (sec) 1.290000 now iterating at: 06:05:11 rms-change max change #iterations 10.25331 331.7399 at 10iterations 6.032188 132.8714 at 20iterations 3.540412 61.91531 at 30iterations 2.075779 39.76534 at 40iterations 1.215045 22.82093 at 50iterations 0.7125509 12.05323 at 60iterations 0.4166076 7.088011 at 70iterations 0.2440441 4.743924 at 80iterations 0.1428214 2.430151 at 90iterations 8.3447292E-02 1.744955 at 100iterations 4.8890781E-02 0.8641379 at 110iterations 2.8587634E-02 0.4946318 at 120iterations 1.6714951E-02 0.2772312 at 130iterations 9.8152729E-03 0.1663532 at 140iterations 5.7469271E-03 9.7861290E-02 at 150iterations 3.3940382E-03 6.3270569E-02 at 160iterations 2.0157727E-03 3.8625717E-02 at 170iterations 1.2146669E-03 2.8455734E-02 at 180iterations finished qdiffx linear iterations at : 06:05:22 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 1.2146669E-03 2.8455734E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 06:05:23 12.601u 0.212s 0:13.08 97.9% 0+0k 0+0io 0pf+0w