Mon Oct 10 16:19:38 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 16:19:38 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 !!! WARNING: GLU 347 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6198096 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): 201.8300 259.0080 ymin,ymax (A): 59.16400 105.8440 zmin,zma (A): 157.6250 215.0620 x,y,z range (A): 57.17799 46.68000 57.43700 scale (grids/A): 0.6198096 object centre (A): 230.4190 82.50400 186.3435 number of atom coordinates read : 2396 total number of charged atoms : 2259 net assigned charge : 9.728024 assigned positive charge : 361.1859 centred at (gu) : 90.17290 91.53706 91.31970 assigned negative charge : -351.4586 centred at (gu) : 90.30494 91.58958 91.41150 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6269 nv = 96 ne = 84 npr = 46602 no. pairs analyzed = 46602 no. exposed pairs = 3260 no. arc points = 23762 no. surface atoms = 1093 nbur = 1303 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 3064 m= 0 mr = 30 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2472 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7624 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0019593E-08 3.0531142E-09 midg,1,midg; midg,igrid,midg 7.9287092E-09 6.5495689E-09 1,midg,midg; igrid,midg,midg 1.5080506E-08 -9.0487604E-11 gauss-seidel spectral radius is 0.9865140 estimated iterations to convergence 70 setup time was (sec) 0.3700000 now iterating at: 16:19:38 rms-change max change #iterations 0.1188113 17.08214 at 10iterations 1.0544963E-02 1.505079 at 20iterations 9.6398353E-04 0.1444778 at 30iterations 8.9454305E-05 1.7506599E-02 at 40iterations 8.1897142E-06 1.3198853E-03 at 50iterations finished qdiffx linear iterations at : 16:19:41 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 8.1897142E-06 1.3198853E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 16:19:42 3.346u 0.165s 0:03.84 91.1% 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 16:19:42 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 !!! WARNING: GLU 347 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.859429 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): 201.8300 259.0080 ymin,ymax (A): 59.16400 105.8440 zmin,zma (A): 157.6250 215.0620 x,y,z range (A): 57.17799 46.68000 57.43700 scale (grids/A): 1.859429 object centre (A): 230.4190 82.50400 186.3435 number of atom coordinates read : 2396 total number of charged atoms : 2259 net assigned charge : 9.728024 assigned positive charge : 361.1859 centred at (gu) : 90.51799 94.61059 93.95866 assigned negative charge : -351.4586 centred at (gu) : 90.91447 94.76846 94.23432 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23762 grid for indexing accessible points = 1.400000 m= 22347 mr = 42353 m= 2943 mr = 15642 m= 142 mr = 1587 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 443 time to turn everything in is 0.3300000 number of dielectric boundary points 32190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 17743 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) : 0.6198096 object centre at (A) : 230.4190 82.50400 186.3435 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4301130E-03 -1.0023855E-04 midg,1,midg; midg,igrid,midg 1.3678823E-02 1.9371049E-02 1,midg,midg; igrid,midg,midg 2.5340240E-02 -2.1474026E-03 gauss-seidel spectral radius is 0.9985586 estimated iterations to convergence 209 setup time was (sec) 0.5400000 now iterating at: 16:19:42 rms-change max change #iterations 3.809783 168.0729 at 10iterations 1.732683 66.38885 at 20iterations 0.7916420 32.17961 at 30iterations 0.3620242 12.04153 at 40iterations 0.1651596 5.943621 at 50iterations 7.5566724E-02 2.416393 at 60iterations 3.4430139E-02 1.155785 at 70iterations 1.5743742E-02 0.5204468 at 80iterations 7.2081955E-03 0.2367897 at 90iterations 3.2940840E-03 0.1128540 at 100iterations 1.5135733E-03 4.8641205E-02 at 110iterations 6.9144164E-04 2.3536682E-02 at 120iterations finished qdiffx linear iterations at : 16:19:49 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 6.9144164E-04 2.3536682E-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) 7.670000 DelPhi exited at 16:19:50 7.677u 0.189s 0:08.14 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 16:19:50 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 !!! WARNING: GLU 347 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.789143 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): 201.8300 259.0080 ymin,ymax (A): 59.16400 105.8440 zmin,zma (A): 157.6250 215.0620 x,y,z range (A): 57.17799 46.68000 57.43700 scale (grids/A): 2.789143 object centre (A): 230.4190 82.50400 186.3435 number of atom coordinates read : 2396 total number of charged atoms : 2259 net assigned charge : 9.728024 assigned positive charge : 361.1859 centred at (gu) : 90.77692 96.91569 95.93787 assigned negative charge : -351.4586 centred at (gu) : 91.37167 97.15268 96.35141 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 152958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23762 grid for indexing accessible points = 1.400000 m= 72289 mr = 103193 m= 24727 mr = 56990 m= 5005 mr = 19194 m= 523 mr = 3432 m= 28 mr = 266 m= 0 mr = 14 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1420 time to turn everything in is 0.8200000 number of dielectric boundary points 72441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 18065 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) : 1.859429 object centre at (A) : 230.4190 82.50400 186.3435 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6388204 -3.8624153E-02 midg,1,midg; midg,igrid,midg 0.1039306 0.1858510 1,midg,midg; igrid,midg,midg 0.1743695 1.6894080E-02 gauss-seidel spectral radius is 0.9992467 estimated iterations to convergence 288 setup time was (sec) 1.050000 now iterating at: 16:19:51 rms-change max change #iterations 9.226526 364.1633 at 10iterations 5.412259 127.2018 at 20iterations 3.131112 73.22460 at 30iterations 1.809633 38.00050 at 40iterations 1.041747 27.90070 at 50iterations 0.5966547 12.07035 at 60iterations 0.3421339 7.638676 at 70iterations 0.1956803 4.144737 at 80iterations 0.1121949 2.415108 at 90iterations 6.4250045E-02 1.290230 at 100iterations 3.6612615E-02 0.7851377 at 110iterations 2.0914763E-02 0.4094467 at 120iterations 1.1903225E-02 0.2504539 at 130iterations 6.8150433E-03 0.1388874 at 140iterations 3.8920003E-03 7.2174072E-02 at 150iterations 2.2207513E-03 4.7503471E-02 at 160iterations 1.2671880E-03 2.4475098E-02 at 170iterations 7.2254706E-04 1.5468597E-02 at 180iterations finished qdiffx linear iterations at : 16:20:02 total time elapsed so far: 12.27000 # loops : 180 mean,max change (kT/e) : 7.2254706E-04 1.5468597E-02 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 16:20:03 12.403u 0.209s 0:12.91 97.5% 0+0k 0+0io 0pf+0w