Mon Oct 10 19:35:32 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 Mon Oct 10 2011 at 19:35:33 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2611 !!! WARNING: HIR 105 has a net charge of 0.5140 !!! WARNING: HIR 231 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6228567 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): -10.23300 45.22000 ymin,ymax (A): -16.97800 36.10400 zmin,zma (A): -11.56000 45.59600 x,y,z range (A): 55.45300 53.08200 57.15600 scale (grids/A): 0.6228567 object centre (A): 17.49350 9.563000 17.01800 number of atom coordinates read : 2611 total number of charged atoms : 2474 net assigned charge : -0.9719917 assigned positive charge : 389.0498 centred at (gu) : 89.29543 90.73055 90.10456 assigned negative charge : -390.0229 centred at (gu) : 89.25040 90.75415 90.12112 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6978 nv = 96 ne = 84 npr = 51955 no. pairs analyzed = 51955 no. exposed pairs = 3762 no. arc points = 26474 no. surface atoms = 1234 nbur = 1377 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 401 mr = 3422 m= 0 mr = 28 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2566 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8334 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7728093E-10 -2.0611537E-09 midg,1,midg; midg,igrid,midg 7.5483081E-10 -2.9696254E-09 1,midg,midg; igrid,midg,midg -4.7865445E-09 2.0770328E-09 gauss-seidel spectral radius is 0.9866678 estimated iterations to convergence 71 setup time was (sec) 0.5500000 now iterating at: 19:35:33 rms-change max change #iterations 0.1262955 21.37903 at 10iterations 1.1600536E-02 1.793915 at 20iterations 1.1111031E-03 0.1484734 at 30iterations 1.1962563E-04 1.8098831E-02 at 40iterations 1.8195713E-05 2.8076172E-03 at 50iterations finished qdiffx linear iterations at : 19:35:36 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.8195713E-05 2.8076172E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 19:35:37 3.421u 0.201s 0:04.24 85.3% 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 Mon Oct 10 2011 at 19:35:37 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2611 !!! WARNING: HIR 105 has a net charge of 0.5140 !!! WARNING: HIR 231 has a net charge of 0.5140 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: 1.868570 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): -10.23300 45.22000 ymin,ymax (A): -16.97800 36.10400 zmin,zma (A): -11.56000 45.59600 x,y,z range (A): 55.45300 53.08200 57.15600 scale (grids/A): 1.868570 object centre (A): 17.49350 9.563000 17.01800 number of atom coordinates read : 2611 total number of charged atoms : 2474 net assigned charge : -0.9719917 assigned positive charge : 389.0498 centred at (gu) : 87.88577 92.19131 90.31301 assigned negative charge : -390.0229 centred at (gu) : 87.75118 92.26212 90.36338 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74385 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 26029 mr = 48278 m= 4196 mr = 17898 m= 238 mr = 2333 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 283 time to turn everything in is 0.5800000 number of dielectric boundary points 36288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19428 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) : 0.6228567 object centre at (A) : 17.49350 9.563000 17.01800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2017624E-02 -2.3617057E-02 midg,1,midg; midg,igrid,midg 1.4631448E-02 -1.1534372E-02 1,midg,midg; igrid,midg,midg -3.1687564E-03 1.6725273E-03 gauss-seidel spectral radius is 0.9986094 estimated iterations to convergence 213 setup time was (sec) 0.9900000 now iterating at: 19:35:38 rms-change max change #iterations 4.155699 191.4695 at 10iterations 1.909856 68.65752 at 20iterations 0.8897137 29.15049 at 30iterations 0.4117032 13.69221 at 40iterations 0.1915348 6.234044 at 50iterations 8.8649727E-02 2.900279 at 60iterations 4.1098122E-02 1.346962 at 70iterations 1.9197213E-02 0.6078320 at 80iterations 8.9330487E-03 0.2781978 at 90iterations 4.1458481E-03 0.1338215 at 100iterations 1.9403758E-03 6.4132690E-02 at 110iterations 9.0586965E-04 2.8208733E-02 at 120iterations finished qdiffx linear iterations at : 19:35:47 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 9.0586965E-04 2.8208733E-02 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.630000 DelPhi exited at 19:35:47 9.628u 0.314s 0:10.30 96.4% 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 Mon Oct 10 2011 at 19:35:47 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2611 !!! WARNING: HIR 105 has a net charge of 0.5140 !!! WARNING: HIR 231 has a net charge of 0.5140 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: 2.802855 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): -10.23300 45.22000 ymin,ymax (A): -16.97800 36.10400 zmin,zma (A): -11.56000 45.59600 x,y,z range (A): 55.45300 53.08200 57.15600 scale (grids/A): 2.802855 object centre (A): 17.49350 9.563000 17.01800 number of atom coordinates read : 2611 total number of charged atoms : 2474 net assigned charge : -0.9719917 assigned positive charge : 389.0498 centred at (gu) : 86.82851 93.28655 90.46938 assigned negative charge : -390.0229 centred at (gu) : 86.62675 93.39326 90.54482 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 171833 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 83144 mr = 118202 m= 30501 mr = 64884 m= 7434 mr = 23301 m= 1027 mr = 5117 m= 35 mr = 554 m= 0 mr = 4 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 968 time to turn everything in is 1.410000 number of dielectric boundary points 81912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 19786 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) : 1.868570 object centre at (A) : 17.49350 9.563000 17.01800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1528914 -0.2191280 midg,1,midg; midg,igrid,midg 0.2142354 -6.4074956E-02 1,midg,midg; igrid,midg,midg 0.1705278 -2.4836976E-02 gauss-seidel spectral radius is 0.9992672 estimated iterations to convergence 292 setup time was (sec) 1.760000 now iterating at: 19:35:49 rms-change max change #iterations 9.981395 363.9177 at 10iterations 5.913498 143.1274 at 20iterations 3.463278 79.49702 at 30iterations 2.029050 44.29340 at 40iterations 1.181210 23.63850 at 50iterations 0.6862698 14.20706 at 60iterations 0.3980496 7.281572 at 70iterations 0.2309422 4.684102 at 80iterations 0.1335523 2.718067 at 90iterations 7.7039994E-02 1.498441 at 100iterations 4.4581909E-02 0.8097954 at 110iterations 2.5701689E-02 0.5048437 at 120iterations 1.4824081E-02 0.2759390 at 130iterations 8.5604712E-03 0.1540680 at 140iterations 4.9411920E-03 9.4688416E-02 at 150iterations 2.8454026E-03 5.4995537E-02 at 160iterations 1.6439600E-03 3.0330658E-02 at 170iterations 9.4938802E-04 1.6544342E-02 at 180iterations finished qdiffx linear iterations at : 19:36:03 total time elapsed so far: 15.10000 # loops : 180 mean,max change (kT/e) : 9.4938802E-04 1.6544342E-02 energy calculations done at 15.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.27000 DelPhi exited at 19:36:03 15.274u 0.341s 0:16.04 97.3% 0+0k 0+0io 0pf+0w