Wed Dec 28 11:06:57 PST 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 Wed Dec 28 2011 at 11:06:58 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 0.6099650 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): -23.86100 34.50300 ymin,ymax (A): -19.93600 20.62200 zmin,zma (A): -3.590000 38.67000 x,y,z range (A): 58.36400 40.55800 42.26000 scale (grids/A): 0.6099650 object centre (A): 5.321001 0.3430004 17.54000 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000004 assigned positive charge : 292.6519 centred at (gu) : 89.88976 90.57656 90.49323 assigned negative charge : -288.6523 centred at (gu) : 89.91386 90.71430 90.66054 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4939 nv = 96 ne = 84 npr = 40123 no. pairs analyzed = 40123 no. exposed pairs = 2545 no. arc points = 17678 no. surface atoms = 859 nbur = 1109 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 250 mr = 2677 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1795 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 5982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5830604E-09 -4.3094284E-09 midg,1,midg; midg,igrid,midg 6.5220345E-09 -3.1110665E-09 1,midg,midg; igrid,midg,midg 3.3983001E-09 1.5098665E-09 gauss-seidel spectral radius is 0.9860313 estimated iterations to convergence 69 setup time was (sec) 0.4700000 now iterating at: 11:06:58 rms-change max change #iterations 0.1024814 16.93703 at 10iterations 8.7813186E-03 1.792983 at 20iterations 7.7067770E-04 0.1294937 at 30iterations 6.9160582E-05 1.1657476E-02 at 40iterations 6.0504963E-06 1.0108948E-03 at 50iterations finished qdiffx linear iterations at : 11:07:01 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 6.0504963E-06 1.0108948E-03 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 11:07:01 3.040u 0.147s 0:03.53 90.0% 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 Wed Dec 28 2011 at 11:07:01 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.829895 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): -23.86100 34.50300 ymin,ymax (A): -19.93600 20.62200 zmin,zma (A): -3.590000 38.67000 x,y,z range (A): 58.36400 40.55800 42.26000 scale (grids/A): 1.829895 object centre (A): 5.321001 0.3430004 17.54000 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000004 assigned positive charge : 292.6519 centred at (gu) : 89.66930 91.72973 91.47947 assigned negative charge : -288.6523 centred at (gu) : 89.74181 92.14298 91.98154 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 53361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17678 grid for indexing accessible points = 1.400000 m= 19642 mr = 36515 m= 2922 mr = 14609 m= 130 mr = 1852 m= 0 mr = 18 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 23061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14372 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) : 0.6099650 object centre at (A) : 5.321001 0.3430004 17.54000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4112633E-03 -7.9561733E-03 midg,1,midg; midg,igrid,midg 8.1093041E-03 -3.6512159E-03 1,midg,midg; igrid,midg,midg 3.8373511E-02 3.6755230E-02 gauss-seidel spectral radius is 0.9984465 estimated iterations to convergence 201 setup time was (sec) 0.6600000 now iterating at: 11:07:02 rms-change max change #iterations 3.352400 149.1335 at 10iterations 1.484796 58.22285 at 20iterations 0.6641775 24.25963 at 30iterations 0.2936846 12.26481 at 40iterations 0.1310941 4.642813 at 50iterations 5.8310170E-02 2.321820 at 60iterations 2.5867704E-02 1.080769 at 70iterations 1.1499459E-02 0.4223518 at 80iterations 5.1258509E-03 0.2143698 at 90iterations 2.2854018E-03 8.3084106E-02 at 100iterations 1.0158926E-03 3.8013458E-02 at 110iterations 4.5191692E-04 1.6843796E-02 at 120iterations finished qdiffx linear iterations at : 11:07:08 total time elapsed so far: 6.500000 # loops : 120 mean,max change (kT/e) : 4.5191692E-04 1.6843796E-02 energy calculations done at 6.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.660000 DelPhi exited at 11:07:08 6.666u 0.154s 0:07.18 94.8% 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 Wed Dec 28 2011 at 11:07:08 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.744843 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): -23.86100 34.50300 ymin,ymax (A): -19.93600 20.62200 zmin,zma (A): -3.590000 38.67000 x,y,z range (A): 58.36400 40.55800 42.26000 scale (grids/A): 2.744843 object centre (A): 5.321001 0.3430004 17.54000 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000004 assigned positive charge : 292.6519 centred at (gu) : 89.50402 92.59450 92.21924 assigned negative charge : -288.6523 centred at (gu) : 89.61276 93.21453 92.97231 start vw surface at 0.1200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 123232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17678 grid for indexing accessible points = 1.400000 m= 63222 mr = 88333 m= 23219 mr = 52056 m= 5281 mr = 18855 m= 568 mr = 4012 m= 17 mr = 323 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 51960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 14683 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) : 1.829895 object centre at (A) : 5.321001 0.3430004 17.54000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9772638E-02 -7.8461297E-02 midg,1,midg; midg,igrid,midg 6.2951595E-02 -2.2454195E-02 1,midg,midg; igrid,midg,midg 0.3979797 0.4431396 gauss-seidel spectral radius is 0.9991908 estimated iterations to convergence 278 setup time was (sec) 1.190000 now iterating at: 11:07:10 rms-change max change #iterations 8.080996 312.3658 at 10iterations 4.615035 135.0103 at 20iterations 2.620436 69.53231 at 30iterations 1.480622 40.30124 at 40iterations 0.8342432 19.61067 at 50iterations 0.4685774 10.77107 at 60iterations 0.2627075 5.844743 at 70iterations 0.1476002 3.069490 at 80iterations 8.2743034E-02 1.755722 at 90iterations 4.6433389E-02 0.9909093 at 100iterations 2.5932493E-02 0.5768623 at 110iterations 1.4564672E-02 0.3130560 at 120iterations 8.1587434E-03 0.1737595 at 130iterations 4.5648692E-03 9.5352173E-02 at 140iterations 2.5516949E-03 5.4832458E-02 at 150iterations 1.4283616E-03 2.9173970E-02 at 160iterations 7.9860864E-04 1.7863274E-02 at 170iterations 4.4759878E-04 1.0295957E-02 at 180iterations finished qdiffx linear iterations at : 11:07:19 total time elapsed so far: 10.11000 # loops : 180 mean,max change (kT/e) : 4.4759878E-04 1.0295957E-02 energy calculations done at 10.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.28000 DelPhi exited at 11:07:19 10.287u 0.161s 0:10.79 96.7% 0+0k 0+0io 0pf+0w