Sat Oct 15 11:26:12 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 Sat Oct 15 2011 at 11:26:12 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3327 !!! WARNING: SEP 90 has a net charge of -0.4750 !!! WARNING: GLM 146 has a net charge of -0.0940 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: 0.5640498 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): -20.89300 32.72200 ymin,ymax (A): -19.06800 30.81100 zmin,zma (A): -14.30100 48.81400 x,y,z range (A): 53.61500 49.87900 63.11500 scale (grids/A): 0.5640498 object centre (A): 5.914500 5.871499 17.25650 number of atom coordinates read : 3327 total number of charged atoms : 3185 net assigned charge : 2.431010 assigned positive charge : 512.1986 centred at (gu) : 90.25287 89.28913 90.88176 assigned negative charge : -509.7693 centred at (gu) : 90.42368 89.24394 90.79723 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6758 nv = 96 ne = 84 npr = 68674 no. pairs analyzed = 68674 no. exposed pairs = 3781 no. arc points = 25867 no. surface atoms = 1290 nbur = 2037 mkacc time = 0.1200000 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 = 1.540000 m= 281 mr = 3797 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2742 ## 339 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8864 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6223772E-10 1.8945021E-09 midg,1,midg; midg,igrid,midg -4.3455597E-10 8.1064022E-10 1,midg,midg; igrid,midg,midg 2.5894360E-09 -2.3965723E-09 gauss-seidel spectral radius is 0.9838029 estimated iterations to convergence 65 setup time was (sec) 0.4600000 now iterating at: 11:26:13 rms-change max change #iterations 9.1238491E-02 15.98575 at 10iterations 6.7501469E-03 0.9557552 at 20iterations 5.4280565E-04 7.7550627E-02 at 30iterations 5.0700841E-05 6.9799423E-03 at 40iterations 6.7863721E-06 1.0628700E-03 at 50iterations finished qdiffx linear iterations at : 11:26:17 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 6.7863721E-06 1.0628700E-03 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 11:26:18 3.780u 0.235s 0:05.12 78.3% 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 Sat Oct 15 2011 at 11:26:18 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3327 !!! WARNING: SEP 90 has a net charge of -0.4750 !!! WARNING: GLM 146 has a net charge of -0.0940 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: 1.692149 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): -20.89300 32.72200 ymin,ymax (A): -19.06800 30.81100 zmin,zma (A): -14.30100 48.81400 x,y,z range (A): 53.61500 49.87900 63.11500 scale (grids/A): 1.692149 object centre (A): 5.914500 5.871499 17.25650 number of atom coordinates read : 3327 total number of charged atoms : 3185 net assigned charge : 2.431010 assigned positive charge : 512.1986 centred at (gu) : 90.75771 87.86649 92.64452 assigned negative charge : -509.7693 centred at (gu) : 91.27095 87.73176 92.39145 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 75669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25867 grid for indexing accessible points = 1.400000 m= 24398 mr = 54216 m= 2798 mr = 17672 m= 104 mr = 1567 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.4000000 number of dielectric boundary points 29489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 309 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 24604 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) : 0.5640498 object centre at (A) : 5.914500 5.871499 17.25650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4509130E-02 1.7979911E-02 midg,1,midg; midg,igrid,midg -9.9680992E-03 2.1903282E-03 1,midg,midg; igrid,midg,midg 2.5463704E-02 -1.0828772E-02 gauss-seidel spectral radius is 0.9983396 estimated iterations to convergence 195 setup time was (sec) 0.6300000 now iterating at: 11:26:19 rms-change max change #iterations 3.856565 180.8406 at 10iterations 1.661066 69.48348 at 20iterations 0.7201971 24.30076 at 30iterations 0.3136690 10.06752 at 40iterations 0.1367735 4.903399 at 50iterations 5.9390869E-02 1.973159 at 60iterations 2.5731564E-02 0.8934975 at 70iterations 1.1149877E-02 0.4393253 at 80iterations 4.8506637E-03 0.1796770 at 90iterations 2.1104168E-03 7.2697639E-02 at 100iterations 9.1543852E-04 3.2033920E-02 at 110iterations 3.9863680E-04 1.2670517E-02 at 120iterations finished qdiffx linear iterations at : 11:26:29 total time elapsed so far: 8.200000 # loops : 120 mean,max change (kT/e) : 3.9863680E-04 1.2670517E-02 energy calculations done at 8.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.320000 DelPhi exited at 11:26:30 8.326u 0.291s 0:12.14 70.9% 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 Sat Oct 15 2011 at 11:26:30 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3327 !!! WARNING: SEP 90 has a net charge of -0.4750 !!! WARNING: GLM 146 has a net charge of -0.0940 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: 2.538224 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): -20.89300 32.72200 ymin,ymax (A): -19.06800 30.81100 zmin,zma (A): -14.30100 48.81400 x,y,z range (A): 53.61500 49.87900 63.11500 scale (grids/A): 2.538224 object centre (A): 5.914500 5.871499 17.25650 number of atom coordinates read : 3327 total number of charged atoms : 3185 net assigned charge : 2.431010 assigned positive charge : 512.1986 centred at (gu) : 91.13654 86.79936 93.96656 assigned negative charge : -509.7693 centred at (gu) : 91.90623 86.59757 93.58712 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 176067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25867 grid for indexing accessible points = 1.400000 m= 84018 mr = 131879 m= 25523 mr = 68884 m= 4573 mr = 19987 m= 426 mr = 3168 m= 16 mr = 243 m= 0 mr = 6 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 96 time to turn everything in is 0.9100000 number of dielectric boundary points 66456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 25456 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) : 1.692149 object centre at (A) : 5.914500 5.871499 17.25650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4713303 0.3528183 midg,1,midg; midg,igrid,midg -0.1631166 5.3512920E-02 1,midg,midg; igrid,midg,midg 0.4271648 -0.1732715 gauss-seidel spectral radius is 0.9991843 estimated iterations to convergence 276 setup time was (sec) 1.150000 now iterating at: 11:26:31 rms-change max change #iterations 9.594143 290.6420 at 10iterations 5.393678 116.0555 at 20iterations 3.038541 63.32533 at 30iterations 1.702192 32.19582 at 40iterations 0.9550364 18.76397 at 50iterations 0.5353816 10.58971 at 60iterations 0.2993971 5.725875 at 70iterations 0.1671498 3.047528 at 80iterations 9.3395226E-02 1.810830 at 90iterations 5.2289478E-02 1.049492 at 100iterations 2.9175425E-02 0.5972748 at 110iterations 1.6296692E-02 0.3155065 at 120iterations 9.1018835E-03 0.1758671 at 130iterations 5.0874911E-03 9.7324371E-02 at 140iterations 2.8428761E-03 5.5281639E-02 at 150iterations 1.5898841E-03 3.1512499E-02 at 160iterations 8.8742870E-04 1.6319275E-02 at 170iterations 4.9620587E-04 9.0942383E-03 at 180iterations finished qdiffx linear iterations at : 11:26:43 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 4.9620587E-04 9.0942383E-03 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 11:26:43 12.859u 0.219s 0:13.46 97.0% 0+0k 0+0io 0pf+0w