Mon Oct 10 09:09:22 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 09:09:22 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1044 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: 0.8730412 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): 25.58200 65.61100 ymin,ymax (A): -12.95400 27.82300 zmin,zma (A): 63.08500 100.2710 x,y,z range (A): 40.02900 40.77700 37.18600 scale (grids/A): 0.8730412 object centre (A): 45.59650 7.434500 81.67800 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 146.3090 centred at (gu) : 90.00038 92.86613 88.13202 assigned negative charge : -144.8090 centred at (gu) : 90.22666 92.54016 88.30984 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6001 nv = 96 ne = 84 npr = 20519 no. pairs analyzed = 20519 no. exposed pairs = 1524 no. arc points = 11272 no. surface atoms = 505 nbur = 539 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 618 mr = 3091 m= 10 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 6.0000010E-02 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.1800000 number of dielectric boundary points 3331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 534 ## 40 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 4774 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4189800E-06 -4.1903058E-07 midg,1,midg; midg,igrid,midg -7.9426439E-07 2.7278857E-06 1,midg,midg; igrid,midg,midg 1.2566670E-06 -8.0505504E-07 gauss-seidel spectral radius is 0.9930460 estimated iterations to convergence 97 setup time was (sec) 0.4000000 now iterating at: 09:09:23 rms-change max change #iterations 0.3067190 52.37758 at 10iterations 5.5240221E-02 8.979853 at 20iterations 9.9811777E-03 1.375084 at 30iterations 1.7983884E-03 0.2468300 at 40iterations 3.1497565E-04 3.8918018E-02 at 50iterations finished qdiffx linear iterations at : 09:09:25 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 3.1497565E-04 3.8918018E-02 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 09:09:26 3.197u 0.202s 0:03.75 90.4% 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 09:09:26 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1044 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: 2.619123 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): 25.58200 65.61100 ymin,ymax (A): -12.95400 27.82300 zmin,zma (A): 63.08500 100.2710 x,y,z range (A): 40.02900 40.77700 37.18600 scale (grids/A): 2.619123 object centre (A): 45.59650 7.434500 81.67800 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 146.3090 centred at (gu) : 90.00114 98.59827 84.39606 assigned negative charge : -144.8090 centred at (gu) : 90.67998 97.62052 84.92960 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11272 grid for indexing accessible points = 1.400000 m= 26563 mr = 38083 m= 8762 mr = 20468 m= 1647 mr = 6824 m= 119 mr = 1065 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 335 time to turn everything in is 0.5100000 number of dielectric boundary points 30536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 7336 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) : 0.8730412 object centre at (A) : 45.59650 7.434500 81.67800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3357412E-02 4.6220720E-03 midg,1,midg; midg,igrid,midg -2.4761898E-02 9.8707505E-02 1,midg,midg; igrid,midg,midg 4.4939920E-02 -2.0577272E-02 gauss-seidel spectral radius is 0.9990932 estimated iterations to convergence 262 setup time was (sec) 0.7900000 now iterating at: 09:09:27 rms-change max change #iterations 4.441968 273.0641 at 10iterations 2.394921 99.95061 at 20iterations 1.284737 40.29285 at 30iterations 0.6875747 20.99384 at 40iterations 0.3709520 11.02018 at 50iterations 0.1984965 6.163887 at 60iterations 0.1065399 3.472282 at 70iterations 5.7209853E-02 1.839409 at 80iterations 3.0759849E-02 0.9259529 at 90iterations 1.6578814E-02 0.4965210 at 100iterations 8.8771628E-03 0.2738647 at 110iterations 4.7913059E-03 0.1399803 at 120iterations finished qdiffx linear iterations at : 09:09:34 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 4.7913059E-03 0.1399803 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 09:09:34 7.453u 0.245s 0:07.99 96.2% 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 09:09:34 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1044 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: 3.928685 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): 25.58200 65.61100 ymin,ymax (A): -12.95400 27.82300 zmin,zma (A): 63.08500 100.2710 x,y,z range (A): 40.02900 40.77700 37.18600 scale (grids/A): 3.928685 object centre (A): 45.59650 7.434500 81.67800 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 146.3090 centred at (gu) : 90.00169 102.8974 81.59411 assigned negative charge : -144.8090 centred at (gu) : 91.01997 101.4308 82.39443 start vw surface at 0.1300000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 136940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11272 grid for indexing accessible points = 1.400000 m= 74670 mr = 91602 m= 40156 mr = 61225 m= 18138 mr = 34532 m= 6005 mr = 15410 m= 1284 mr = 4868 m= 189 mr = 909 m= 21 mr = 131 m= 0 mr = 16 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 1137 time to turn everything in is 1.640000 number of dielectric boundary points 68710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 7344 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) : 2.619123 object centre at (A) : 45.59650 7.434500 81.67800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3223325E-02 9.0232052E-02 midg,1,midg; midg,igrid,midg -0.1192915 0.5097441 1,midg,midg; igrid,midg,midg 0.1836860 -0.1203048 gauss-seidel spectral radius is 0.9993589 estimated iterations to convergence 311 setup time was (sec) 1.930000 now iterating at: 09:09:36 rms-change max change #iterations 9.179070 278.1876 at 10iterations 5.533448 126.9387 at 20iterations 3.328786 81.82227 at 30iterations 1.994646 42.13514 at 40iterations 1.193560 25.34532 at 50iterations 0.7137255 14.58423 at 60iterations 0.4266894 8.511456 at 70iterations 0.2547504 4.836535 at 80iterations 0.1520984 3.036987 at 90iterations 9.0940788E-02 1.917874 at 100iterations 5.4370224E-02 1.117597 at 110iterations 3.2413859E-02 0.5948687 at 120iterations 1.9334484E-02 0.3563557 at 130iterations 1.1533393E-02 0.2230883 at 140iterations 6.8806298E-03 0.1304655 at 150iterations 4.1069984E-03 7.5810432E-02 at 160iterations 2.4476724E-03 4.4031143E-02 at 170iterations 1.4626759E-03 2.5192261E-02 at 180iterations finished qdiffx linear iterations at : 09:09:47 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 1.4626759E-03 2.5192261E-02 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 09:09:47 12.442u 0.238s 0:13.00 97.4% 0+0k 0+0io 0pf+0w