Mon Oct 10 14:02:27 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 14:02:27 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: 372 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4612 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5450176 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): 16.97500 79.11200 ymin,ymax (A): 119.6840 185.0030 zmin,zma (A): -1.708000 59.79800 x,y,z range (A): 62.13700 65.31899 61.50600 scale (grids/A): 0.5450176 object centre (A): 48.04350 152.3435 29.04500 number of atom coordinates read : 4612 total number of charged atoms : 4435 net assigned charge : 2.906037 assigned positive charge : 707.4896 centred at (gu) : 91.65119 89.19326 87.25728 assigned negative charge : -704.5868 centred at (gu) : 91.61219 89.10804 87.27245 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8867 nv = 96 ne = 84 npr = 91935 no. pairs analyzed = 91935 no. exposed pairs = 5573 no. arc points = 38688 no. surface atoms = 1879 nbur = 2733 mkacc time = 0.1600000 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= 409 mr = 4802 m= 4 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.3100000 number of dielectric boundary points 4446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4040 ## 544 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11785 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3459366E-10 1.0711446E-11 midg,1,midg; midg,igrid,midg -8.5447532E-10 8.2828605E-10 1,midg,midg; igrid,midg,midg -1.4650386E-10 8.4253871E-10 gauss-seidel spectral radius is 0.9827666 estimated iterations to convergence 63 setup time was (sec) 0.5000000 now iterating at: 14:02:28 rms-change max change #iterations 9.1440931E-02 14.89611 at 10iterations 6.4371899E-03 0.8418617 at 20iterations 5.8738957E-04 8.4364891E-02 at 30iterations 1.3012270E-04 1.7583847E-02 at 40iterations 4.2398238E-05 6.0129166E-03 at 50iterations finished qdiffx linear iterations at : 14:02:31 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 4.2398238E-05 6.0129166E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 14:02:32 3.486u 0.186s 0:04.62 79.2% 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 14:02:32 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: 372 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4612 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.635053 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): 16.97500 79.11200 ymin,ymax (A): 119.6840 185.0030 zmin,zma (A): -1.708000 59.79800 x,y,z range (A): 62.13700 65.31899 61.50600 scale (grids/A): 1.635053 object centre (A): 48.04350 152.3435 29.04500 number of atom coordinates read : 4612 total number of charged atoms : 4435 net assigned charge : 2.906037 assigned positive charge : 707.4896 centred at (gu) : 94.95218 87.57872 81.77069 assigned negative charge : -704.5868 centred at (gu) : 94.83611 87.32389 81.81715 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 99727 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38688 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31693 mr = 69970 m= 3656 mr = 22188 m= 114 mr = 1972 m= 0 mr = 20 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1618 time to turn everything in is 0.4700000 number of dielectric boundary points 41040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 482 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 33981 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) : 0.5450176 object centre at (A) : 48.04350 152.3435 29.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5674867E-03 9.4617261E-03 midg,1,midg; midg,igrid,midg 1.3702455E-02 3.1194968E-02 1,midg,midg; igrid,midg,midg -1.1161173E-02 -1.5414601E-02 gauss-seidel spectral radius is 0.9983470 estimated iterations to convergence 195 setup time was (sec) 0.6900000 now iterating at: 14:02:33 rms-change max change #iterations 4.359115 205.2505 at 10iterations 1.887055 93.76015 at 20iterations 0.8175480 32.64382 at 30iterations 0.3551510 13.21093 at 40iterations 0.1546232 5.639320 at 50iterations 6.7039825E-02 2.099426 at 60iterations 2.9168963E-02 0.8743744 at 70iterations 1.2689104E-02 0.3652439 at 80iterations 5.5287010E-03 0.1656342 at 90iterations 2.4181118E-03 6.8687439E-02 at 100iterations 1.0647778E-03 3.0208588E-02 at 110iterations 4.7220537E-04 1.4343262E-02 at 120iterations finished qdiffx linear iterations at : 14:02:40 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 4.7220537E-04 1.4343262E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 14:02:40 8.142u 0.218s 0:08.84 94.4% 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 14:02:41 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: 372 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4612 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.452579 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): 16.97500 79.11200 ymin,ymax (A): 119.6840 185.0030 zmin,zma (A): -1.708000 59.79800 x,y,z range (A): 62.13700 65.31899 61.50600 scale (grids/A): 2.452579 object centre (A): 48.04350 152.3435 29.04500 number of atom coordinates read : 4612 total number of charged atoms : 4435 net assigned charge : 2.906037 assigned positive charge : 707.4896 centred at (gu) : 97.42799 86.36787 77.65572 assigned negative charge : -704.5868 centred at (gu) : 97.25407 85.98580 77.72573 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 232468 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38688 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 109493 mr = 171411 m= 32308 mr = 87647 m= 6126 mr = 24627 m= 504 mr = 4326 m= 9 mr = 269 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 5423 time to turn everything in is 1.210000 number of dielectric boundary points 92628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 35424 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) : 1.635053 object centre at (A) : 48.04350 152.3435 29.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7959850E-02 0.1798182 midg,1,midg; midg,igrid,midg 0.2204309 0.5809559 1,midg,midg; igrid,midg,midg -0.1579949 -0.2844096 gauss-seidel spectral radius is 0.9992186 estimated iterations to convergence 282 setup time was (sec) 1.450000 now iterating at: 14:02:42 rms-change max change #iterations 11.21487 338.2602 at 10iterations 6.492511 131.9074 at 20iterations 3.735269 77.41496 at 30iterations 2.142661 41.00135 at 40iterations 1.224711 24.49677 at 50iterations 0.6983986 13.36702 at 60iterations 0.3981111 7.163636 at 70iterations 0.2257676 4.232202 at 80iterations 0.1283354 2.152719 at 90iterations 7.2872184E-02 1.296497 at 100iterations 4.1333791E-02 0.7244663 at 110iterations 2.3454802E-02 0.4319553 at 120iterations 1.3269976E-02 0.2483120 at 130iterations 7.5197532E-03 0.1218796 at 140iterations 4.2707464E-03 8.1121922E-02 at 150iterations 2.4204045E-03 4.0606499E-02 at 160iterations 1.3757979E-03 2.3525238E-02 at 170iterations 7.8590156E-04 1.4431953E-02 at 180iterations finished qdiffx linear iterations at : 14:02:54 total time elapsed so far: 13.24000 # loops : 180 mean,max change (kT/e) : 7.8590156E-04 1.4431953E-02 energy calculations done at 13.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.38000 DelPhi exited at 14:02:55 13.383u 0.208s 0:14.40 94.3% 0+0k 0+0io 0pf+0w