Tue Oct 11 01:10:12 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 01:10:12 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 = 2740 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: 0.6321135 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): -4.947000 51.37200 ymin,ymax (A): -16.15700 29.77200 zmin,zma (A): 56.87200 109.7430 x,y,z range (A): 56.31900 45.92900 52.87101 scale (grids/A): 0.6321135 object centre (A): 23.21250 6.807501 83.30750 number of atom coordinates read : 2740 total number of charged atoms : 2596 net assigned charge : 4.500017 assigned positive charge : 412.4155 centred at (gu) : 89.83530 90.14054 89.06592 assigned negative charge : -407.9162 centred at (gu) : 90.08671 90.05491 89.10202 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7272 nv = 96 ne = 84 npr = 55631 no. pairs analyzed = 55631 no. exposed pairs = 3290 no. arc points = 23083 no. surface atoms = 1119 nbur = 1621 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 375 mr = 4091 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3600000 number of dielectric boundary points 3526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2230 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8753 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0627375E-08 1.3293140E-09 midg,1,midg; midg,igrid,midg -3.2645895E-09 1.3931236E-08 1,midg,midg; igrid,midg,midg 3.0338505E-08 -1.9607921E-08 gauss-seidel spectral radius is 0.9870467 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 01:10:13 rms-change max change #iterations 0.1384177 18.77621 at 10iterations 1.4738980E-02 2.090084 at 20iterations 1.9267227E-03 0.3467674 at 30iterations 4.3418229E-04 9.0751648E-02 at 40iterations 1.1816875E-04 2.5684357E-02 at 50iterations finished qdiffx linear iterations at : 01:10:17 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.1816875E-04 2.5684357E-02 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 01:10:17 4.068u 0.278s 0:05.05 85.7% 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 Tue Oct 11 2011 at 01:10:18 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 = 2740 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: 1.896340 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): -4.947000 51.37200 ymin,ymax (A): -16.15700 29.77200 zmin,zma (A): 56.87200 109.7430 x,y,z range (A): 56.31900 45.92900 52.87101 scale (grids/A): 1.896340 object centre (A): 23.21250 6.807501 83.30750 number of atom coordinates read : 2740 total number of charged atoms : 2596 net assigned charge : 4.500017 assigned positive charge : 412.4155 centred at (gu) : 89.50498 90.42100 87.19711 assigned negative charge : -407.9162 centred at (gu) : 90.25983 90.16431 87.30560 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 79128 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23083 grid for indexing accessible points = 1.400000 m= 28031 mr = 55505 m= 4177 mr = 20832 m= 213 mr = 2657 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 467 time to turn everything in is 0.6800000 number of dielectric boundary points 32500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 20389 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) : 0.6321135 object centre at (A) : 23.21250 6.807501 83.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0996455E-03 1.5525218E-02 midg,1,midg; midg,igrid,midg 1.1697751E-02 2.0412473E-02 1,midg,midg; igrid,midg,midg 4.1049242E-02 -3.8089070E-02 gauss-seidel spectral radius is 0.9986347 estimated iterations to convergence 214 setup time was (sec) 0.9800000 now iterating at: 01:10:19 rms-change max change #iterations 4.356917 194.3484 at 10iterations 2.038445 68.94373 at 20iterations 0.9533127 32.95698 at 30iterations 0.4463661 15.92340 at 40iterations 0.2096296 5.826902 at 50iterations 9.8248221E-02 3.310934 at 60iterations 4.6243567E-02 1.402050 at 70iterations 2.1797428E-02 0.6543007 at 80iterations 1.0349210E-02 0.3178177 at 90iterations 4.9943132E-03 0.1670094 at 100iterations 2.4780550E-03 8.5418701E-02 at 110iterations 1.2886862E-03 4.9417496E-02 at 120iterations finished qdiffx linear iterations at : 01:10:27 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 1.2886862E-03 4.9417496E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 01:10:28 9.373u 0.314s 0:10.17 95.1% 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 01:10:28 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 = 2740 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: 2.844511 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): -4.947000 51.37200 ymin,ymax (A): -16.15700 29.77200 zmin,zma (A): 56.87200 109.7430 x,y,z range (A): 56.31900 45.92900 52.87101 scale (grids/A): 2.844511 object centre (A): 23.21250 6.807501 83.30750 number of atom coordinates read : 2740 total number of charged atoms : 2596 net assigned charge : 4.500017 assigned positive charge : 412.4155 centred at (gu) : 89.25742 90.63113 85.79554 assigned negative charge : -407.9162 centred at (gu) : 90.38972 90.24635 85.95817 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 183049 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23083 grid for indexing accessible points = 1.400000 m= 91926 mr = 134457 m= 32203 mr = 75625 m= 7439 mr = 25952 m= 896 mr = 5592 m= 37 mr = 574 m= 0 mr = 6 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1679 time to turn everything in is 1.780000 number of dielectric boundary points 73344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 20767 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) : 1.896340 object centre at (A) : 23.21250 6.807501 83.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7872341E-02 0.1678777 midg,1,midg; midg,igrid,midg 0.1837405 0.2263315 1,midg,midg; igrid,midg,midg 0.4933450 -0.2153569 gauss-seidel spectral radius is 0.9992558 estimated iterations to convergence 289 setup time was (sec) 2.110000 now iterating at: 01:10:30 rms-change max change #iterations 10.08719 409.3415 at 10iterations 5.852655 129.6609 at 20iterations 3.379350 83.70897 at 30iterations 1.949517 36.70705 at 40iterations 1.122082 23.49500 at 50iterations 0.6453832 11.87520 at 60iterations 0.3709418 6.364855 at 70iterations 0.2132784 3.850204 at 80iterations 0.1224458 2.069668 at 90iterations 7.0544876E-02 1.237108 at 100iterations 4.0443476E-02 0.6748047 at 110iterations 2.3300977E-02 0.4079514 at 120iterations 1.3471425E-02 0.2455139 at 130iterations 7.8523103E-03 0.1489449 at 140iterations 4.6361992E-03 9.1178894E-02 at 150iterations 2.7890585E-03 5.8845520E-02 at 160iterations 1.7428712E-03 3.8959503E-02 at 170iterations 1.1478205E-03 2.5775909E-02 at 180iterations finished qdiffx linear iterations at : 01:10:44 total time elapsed so far: 15.60000 # loops : 180 mean,max change (kT/e) : 1.1478205E-03 2.5775909E-02 energy calculations done at 15.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.78000 DelPhi exited at 01:10:44 15.785u 0.295s 0:16.57 96.9% 0+0k 0+0io 0pf+0w