Sun Oct 9 18:44:58 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 Sun Oct 9 2011 at 18:44:58 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5299 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5497899 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): 3.184000 67.93600 ymin,ymax (A): -9.127000 54.33200 zmin,zma (A): -1.025000 63.45500 x,y,z range (A): 64.75201 63.45900 64.48000 scale (grids/A): 0.5497899 object centre (A): 35.56000 22.60250 31.21500 number of atom coordinates read : 5299 total number of charged atoms : 5164 net assigned charge : 2.649038 assigned positive charge : 821.6680 centred at (gu) : 88.03849 89.08251 89.06902 assigned negative charge : -819.0255 centred at (gu) : 87.89679 89.12265 88.97658 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 10311 nv = 96 ne = 84 npr = 107731 no. pairs analyzed = 107731 no. exposed pairs = 6141 no. arc points = 41831 no. surface atoms = 2097 nbur = 3202 mkacc time = 0.2900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 472 mr = 5922 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 4836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4228 ## 478 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 13673 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3496576E-09 1.2094088E-09 midg,1,midg; midg,igrid,midg 1.0081189E-09 -2.5400393E-10 1,midg,midg; igrid,midg,midg -2.9265699E-09 1.3527023E-09 gauss-seidel spectral radius is 0.9831048 estimated iterations to convergence 63 setup time was (sec) 0.8200000 now iterating at: 18:44:59 rms-change max change #iterations 0.1079549 14.26350 at 10iterations 9.5239403E-03 1.291809 at 20iterations 2.5898144E-03 0.2773666 at 30iterations 1.1445507E-03 0.1295669 at 40iterations 5.2661361E-04 6.3725471E-02 at 50iterations finished qdiffx linear iterations at : 18:45:03 total time elapsed so far: 4.770000 # loops : 50 mean,max change (kT/e) : 5.2661361E-04 6.3725471E-02 energy calculations done at 4.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.930000 DelPhi exited at 18:45:03 4.937u 0.384s 0:05.63 94.3% 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 Sun Oct 9 2011 at 18:45:03 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5299 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.649370 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): 3.184000 67.93600 ymin,ymax (A): -9.127000 54.33200 zmin,zma (A): -1.025000 63.45500 x,y,z range (A): 64.75201 63.45900 64.48000 scale (grids/A): 1.649370 object centre (A): 35.56000 22.60250 31.21500 number of atom coordinates read : 5299 total number of charged atoms : 5164 net assigned charge : 2.649038 assigned positive charge : 821.6680 centred at (gu) : 84.11395 87.24627 87.20536 assigned negative charge : -819.0255 centred at (gu) : 83.69008 87.36796 86.92967 start vw surface at 0.1700000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 115715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41831 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 39033 mr = 83937 m= 4558 mr = 28140 m= 132 mr = 2400 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.9200000 number of dielectric boundary points 44945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 397 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 39630 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) : 0.5497899 object centre at (A) : 35.56000 22.60250 31.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0185964E-02 1.7750818E-02 midg,1,midg; midg,igrid,midg 2.5049137E-02 7.3779020E-03 1,midg,midg; igrid,midg,midg -2.6470393E-02 1.6537005E-02 gauss-seidel spectral radius is 0.9984251 estimated iterations to convergence 200 setup time was (sec) 1.330000 now iterating at: 18:45:05 rms-change max change #iterations 4.895148 156.1718 at 10iterations 2.174545 71.19862 at 20iterations 0.9625323 26.83805 at 30iterations 0.4288653 11.84876 at 40iterations 0.1898472 5.418688 at 50iterations 8.4873706E-02 2.231838 at 60iterations 3.8069669E-02 1.169647 at 70iterations 1.7433301E-02 0.5490937 at 80iterations 8.3222780E-03 0.2258759 at 90iterations 4.3768156E-03 0.1242847 at 100iterations 2.6334189E-03 6.7214966E-02 at 110iterations 1.7811656E-03 4.6703339E-02 at 120iterations finished qdiffx linear iterations at : 18:45:15 total time elapsed so far: 11.25000 # loops : 120 mean,max change (kT/e) : 1.7811656E-03 4.6703339E-02 energy calculations done at 11.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.42000 DelPhi exited at 18:45:16 11.429u 0.447s 0:12.15 97.6% 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 Sun Oct 9 2011 at 18:45:16 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5299 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.474055 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): 3.184000 67.93600 ymin,ymax (A): -9.127000 54.33200 zmin,zma (A): -1.025000 63.45500 x,y,z range (A): 64.75201 63.45900 64.48000 scale (grids/A): 2.474055 object centre (A): 35.56000 22.60250 31.21500 number of atom coordinates read : 5299 total number of charged atoms : 5164 net assigned charge : 2.649038 assigned positive charge : 821.6680 centred at (gu) : 81.17072 85.86897 85.80773 assigned negative charge : -819.0255 centred at (gu) : 80.53521 86.05180 85.39446 start vw surface at 0.1800000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 269097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41831 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 133304 mr = 204354 m= 41113 mr = 108550 m= 7335 mr = 31813 m= 589 mr = 4993 m= 15 mr = 294 m= 0 mr = 2 time to grow re-entrant surface = 1.500000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 2.380000 number of dielectric boundary points 101447 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 2.530000 number of grid points assigned charge 41264 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) : 1.649370 object centre at (A) : 35.56000 22.60250 31.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4884823 0.3960265 midg,1,midg; midg,igrid,midg 0.2519494 1.5931524E-02 1,midg,midg; igrid,midg,midg -0.5151932 0.1728340 gauss-seidel spectral radius is 0.9992533 estimated iterations to convergence 289 setup time was (sec) 2.740000 now iterating at: 18:45:19 rms-change max change #iterations 12.47355 315.1833 at 10iterations 7.358822 155.6184 at 20iterations 4.307083 83.56052 at 30iterations 2.510203 44.21642 at 40iterations 1.458781 26.06456 at 50iterations 0.8449172 15.88213 at 60iterations 0.4888569 7.939838 at 70iterations 0.2820693 5.040459 at 80iterations 0.1627219 2.434593 at 90iterations 9.3973160E-02 1.400816 at 100iterations 5.4063223E-02 0.9093742 at 110iterations 3.1272188E-02 0.4801064 at 120iterations 1.8165730E-02 0.2773819 at 130iterations 1.0687639E-02 0.1822557 at 140iterations 6.4099412E-03 0.1120052 at 150iterations 4.0010866E-03 6.9946289E-02 at 160iterations 2.6385160E-03 5.0192595E-02 at 170iterations 1.8732754E-03 3.2892227E-02 at 180iterations finished qdiffx linear iterations at : 18:45:37 total time elapsed so far: 21.08000 # loops : 180 mean,max change (kT/e) : 1.8732754E-03 3.2892227E-02 energy calculations done at 21.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.23000 DelPhi exited at 18:45:38 21.239u 0.493s 0:22.09 98.3% 0+0k 0+0io 0pf+0w