Mon Oct 10 09:10:49 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 Mon Oct 10 2011 at 09:10:49 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 = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6320686 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): -35.11700 10.05800 ymin,ymax (A): 1.027000 42.85800 zmin,zma (A): -0.8770000 55.44600 x,y,z range (A): 45.17500 41.83100 56.32300 scale (grids/A): 0.6320686 object centre (A): -12.52950 21.94250 27.28450 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 286.2651 centred at (gu) : 90.40886 89.12571 90.37048 assigned negative charge : -283.2653 centred at (gu) : 90.33846 89.27436 90.41458 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5390 nv = 96 ne = 84 npr = 40208 no. pairs analyzed = 40208 no. exposed pairs = 2529 no. arc points = 17498 no. surface atoms = 862 nbur = 1100 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 2914 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1731 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6284 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8838872E-09 3.4799807E-10 midg,1,midg; midg,igrid,midg 1.6186762E-08 -5.7202429E-09 1,midg,midg; igrid,midg,midg -1.3424793E-09 8.8979748E-09 gauss-seidel spectral radius is 0.9869797 estimated iterations to convergence 72 setup time was (sec) 0.3500000 now iterating at: 09:10:49 rms-change max change #iterations 0.1173071 21.93163 at 10iterations 1.1203434E-02 1.754940 at 20iterations 1.0454903E-03 0.1487083 at 30iterations 1.0125912E-04 1.6250610E-02 at 40iterations 9.5641581E-06 1.7766953E-03 at 50iterations finished qdiffx linear iterations at : 09:10:52 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 9.5641581E-06 1.7766953E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 09:10:53 3.387u 0.208s 0:03.88 92.2% 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 09:10:53 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 = 1962 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: 1.896206 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): -35.11700 10.05800 ymin,ymax (A): 1.027000 42.85800 zmin,zma (A): -0.8770000 55.44600 x,y,z range (A): 45.17500 41.83100 56.32300 scale (grids/A): 1.896206 object centre (A): -12.52950 21.94250 27.28450 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 286.2651 centred at (gu) : 91.22674 87.37720 91.11126 assigned negative charge : -283.2653 centred at (gu) : 91.01580 87.82329 91.24395 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 57380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17498 grid for indexing accessible points = 1.400000 m= 21629 mr = 39146 m= 3638 mr = 16105 m= 222 mr = 2363 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 312 time to turn everything in is 0.3000000 number of dielectric boundary points 25176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 14306 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) : 0.6320686 object centre at (A) : -12.52950 21.94250 27.28450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5497537E-02 3.4747049E-02 midg,1,midg; midg,igrid,midg 7.8828335E-03 -7.4803322E-03 1,midg,midg; igrid,midg,midg -7.9158004E-03 -2.2921560E-03 gauss-seidel spectral radius is 0.9985502 estimated iterations to convergence 208 setup time was (sec) 0.5000000 now iterating at: 09:10:53 rms-change max change #iterations 3.501143 145.8116 at 10iterations 1.606170 63.13253 at 20iterations 0.7372174 26.14385 at 30iterations 0.3359847 12.15170 at 40iterations 0.1528765 5.335539 at 50iterations 7.0297033E-02 2.494078 at 60iterations 3.2088358E-02 1.191978 at 70iterations 1.4648333E-02 0.6336403 at 80iterations 6.7171189E-03 0.2503653 at 90iterations 3.0728963E-03 0.1128554 at 100iterations 1.4091190E-03 5.4582596E-02 at 110iterations 6.4072007E-04 2.1718025E-02 at 120iterations finished qdiffx linear iterations at : 09:11:00 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 6.4072007E-04 2.1718025E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 09:11:01 7.680u 0.224s 0:08.39 94.1% 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 Mon Oct 10 2011 at 09:11:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.844309 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): -35.11700 10.05800 ymin,ymax (A): 1.027000 42.85800 zmin,zma (A): -0.8770000 55.44600 x,y,z range (A): 45.17500 41.83100 56.32300 scale (grids/A): 2.844309 object centre (A): -12.52950 21.94250 27.28450 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 286.2651 centred at (gu) : 91.84009 86.06583 91.66694 assigned negative charge : -283.2653 centred at (gu) : 91.52373 86.73493 91.86592 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 132311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17498 grid for indexing accessible points = 1.400000 m= 67977 mr = 94551 m= 26470 mr = 55749 m= 6550 mr = 21673 m= 921 mr = 5004 m= 45 mr = 602 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 1077 time to turn everything in is 0.7600000 number of dielectric boundary points 56679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 14550 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) : 1.896206 object centre at (A) : -12.52950 21.94250 27.28450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4174822E-02 0.2627859 midg,1,midg; midg,igrid,midg -4.8213508E-03 -9.3940370E-02 1,midg,midg; igrid,midg,midg -0.1126803 -6.8299197E-02 gauss-seidel spectral radius is 0.9992210 estimated iterations to convergence 283 setup time was (sec) 0.9900000 now iterating at: 09:11:02 rms-change max change #iterations 8.321350 417.1244 at 10iterations 4.785166 122.1108 at 20iterations 2.725697 58.89520 at 30iterations 1.557077 32.93353 at 40iterations 0.8824425 20.72406 at 50iterations 0.5001163 10.34392 at 60iterations 0.2843308 6.210412 at 70iterations 0.1608702 3.208691 at 80iterations 9.1169745E-02 1.828140 at 90iterations 5.1682286E-02 1.150488 at 100iterations 2.9167514E-02 0.5599937 at 110iterations 1.6517147E-02 0.3739884 at 120iterations 9.3458937E-03 0.2031194 at 130iterations 5.2843047E-03 0.1125340 at 140iterations 2.9892365E-03 6.1418533E-02 at 150iterations 1.6915939E-03 3.7292480E-02 at 160iterations 9.5451542E-04 2.2935867E-02 at 170iterations 5.4110581E-04 1.0356903E-02 at 180iterations finished qdiffx linear iterations at : 09:11:13 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 5.4110581E-04 1.0356903E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 09:11:14 12.194u 0.209s 0:12.81 96.7% 0+0k 0+0io 0pf+0w