Tue Oct 11 08:10:52 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 Tue Oct 11 2011 at 08:10:52 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1178 !!! WARNING: GLM 319 has a net charge of -0.0940 !!! WARNING: HIZ 320 has a net charge of 0.2000 !!! WARNING: ZN3 355 has a net charge of 1.4000 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: 0.8283308 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): -38.20000 3.353000 ymin,ymax (A): -46.44300 -3.465000 zmin,zma (A): -24.35800 12.78200 x,y,z range (A): 41.55300 42.97800 37.14000 scale (grids/A): 0.8283308 object centre (A): -17.42350 -24.95400 -5.788000 number of atom coordinates read : 1178 total number of charged atoms : 1041 net assigned charge : 6.0055256E-03 assigned positive charge : 168.9171 centred at (gu) : 89.94897 86.94666 91.25008 assigned negative charge : -168.9111 centred at (gu) : 89.91026 87.05362 91.57437 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5460 nv = 96 ne = 84 npr = 24542 no. pairs analyzed = 24542 no. exposed pairs = 1539 no. arc points = 10938 no. surface atoms = 520 nbur = 658 mkacc time = 5.9999995E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 2865 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.1800000 number of dielectric boundary points 2948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 620 ## 40 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 5000 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7890244E-07 -1.0976352E-06 midg,1,midg; midg,igrid,midg 4.9175122E-07 -1.6730934E-07 1,midg,midg; igrid,midg,midg -9.9238378E-08 1.0623685E-07 gauss-seidel spectral radius is 0.9922951 estimated iterations to convergence 92 setup time was (sec) 0.4700000 now iterating at: 08:10:53 rms-change max change #iterations 0.2980415 44.96452 at 10iterations 4.8690483E-02 7.116722 at 20iterations 7.9675121E-03 1.264427 at 30iterations 1.3079939E-03 0.1920862 at 40iterations 2.1304544E-04 2.9994965E-02 at 50iterations finished qdiffx linear iterations at : 08:10:57 total time elapsed so far: 4.820000 # loops : 50 mean,max change (kT/e) : 2.1304544E-04 2.9994965E-02 energy calculations done at 4.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.990000 DelPhi exited at 08:10:58 4.991u 0.400s 0:06.25 86.2% 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 Tue Oct 11 2011 at 08:10:58 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1178 !!! WARNING: GLM 319 has a net charge of -0.0940 !!! WARNING: HIZ 320 has a net charge of 0.2000 !!! WARNING: ZN3 355 has a net charge of 1.4000 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: 2.484993 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): -38.20000 3.353000 ymin,ymax (A): -46.44300 -3.465000 zmin,zma (A): -24.35800 12.78200 x,y,z range (A): 41.55300 42.97800 37.14000 scale (grids/A): 2.484993 object centre (A): -17.42350 -24.95400 -5.788000 number of atom coordinates read : 1178 total number of charged atoms : 1041 net assigned charge : 6.0055256E-03 assigned positive charge : 168.9171 centred at (gu) : 89.84695 80.84015 93.75037 assigned negative charge : -168.9111 centred at (gu) : 89.73074 81.16095 94.72315 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 56518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10938 grid for indexing accessible points = 1.400000 m= 21711 mr = 36970 m= 5292 mr = 16224 m= 677 mr = 3762 m= 30 mr = 377 m= 0 mr = 9 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1720 time to turn everything in is 0.5400000 number of dielectric boundary points 26886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 8315 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) : 0.8283308 object centre at (A) : -17.42350 -24.95400 -5.788000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9386259E-02 -3.9955560E-02 midg,1,midg; midg,igrid,midg -3.3468306E-02 -1.4660857E-02 1,midg,midg; igrid,midg,midg -3.9017221E-04 -1.4255781E-02 gauss-seidel spectral radius is 0.9990205 estimated iterations to convergence 253 setup time was (sec) 0.8300000 now iterating at: 08:10:59 rms-change max change #iterations 4.476069 239.1751 at 10iterations 2.344065 82.51254 at 20iterations 1.230247 42.52674 at 30iterations 0.6439193 19.06139 at 40iterations 0.3388651 10.80786 at 50iterations 0.1774228 5.665058 at 60iterations 9.3449399E-02 3.180816 at 70iterations 4.9001690E-02 1.524154 at 80iterations 2.5675928E-02 0.8858299 at 90iterations 1.3490744E-02 0.4570484 at 100iterations 7.0791366E-03 0.2473869 at 110iterations 3.7207238E-03 0.1284676 at 120iterations finished qdiffx linear iterations at : 08:11:11 total time elapsed so far: 12.04000 # loops : 120 mean,max change (kT/e) : 3.7207238E-03 0.1284676 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 08:11:12 12.218u 0.460s 0:13.55 93.5% 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 Tue Oct 11 2011 at 08:11:12 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1178 !!! WARNING: GLM 319 has a net charge of -0.0940 !!! WARNING: HIZ 320 has a net charge of 0.2000 !!! WARNING: ZN3 355 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.727489 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): -38.20000 3.353000 ymin,ymax (A): -46.44300 -3.465000 zmin,zma (A): -24.35800 12.78200 x,y,z range (A): 41.55300 42.97800 37.14000 scale (grids/A): 3.727489 object centre (A): -17.42350 -24.95400 -5.788000 number of atom coordinates read : 1178 total number of charged atoms : 1041 net assigned charge : 6.0055256E-03 assigned positive charge : 168.9171 centred at (gu) : 89.77055 76.26023 95.62550 assigned negative charge : -168.9111 centred at (gu) : 89.59608 76.74139 97.08479 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 130164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10938 grid for indexing accessible points = 1.400000 m= 65305 mr = 89590 m= 29572 mr = 53118 m= 10316 mr = 24625 m= 2621 mr = 8219 m= 407 mr = 1959 m= 37 mr = 284 m= 0 mr = 16 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 5536 time to turn everything in is 1.580000 number of dielectric boundary points 60611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 8328 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) : 2.484993 object centre at (A) : -17.42350 -24.95400 -5.788000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4749261 -0.3028886 midg,1,midg; midg,igrid,midg -0.1139755 -3.5825070E-02 1,midg,midg; igrid,midg,midg 9.8614700E-02 -0.2367796 gauss-seidel spectral radius is 0.9993373 estimated iterations to convergence 306 setup time was (sec) 1.900000 now iterating at: 08:11:14 rms-change max change #iterations 9.228177 242.3431 at 10iterations 5.465408 130.3627 at 20iterations 3.229843 66.20894 at 30iterations 1.907047 36.40044 at 40iterations 1.128627 21.21229 at 50iterations 0.6650982 12.60370 at 60iterations 0.3927516 6.925089 at 70iterations 0.2320803 4.209377 at 80iterations 0.1366985 2.462448 at 90iterations 8.0994606E-02 1.647106 at 100iterations 4.7708768E-02 0.8953781 at 110iterations 2.8107654E-02 0.5108643 at 120iterations 1.6635802E-02 0.2988510 at 130iterations 9.8494692E-03 0.1788330 at 140iterations 5.8039310E-03 0.1117134 at 150iterations 3.4372753E-03 6.7331314E-02 at 160iterations 2.0311987E-03 3.7242889E-02 at 170iterations 1.2018869E-03 2.0996094E-02 at 180iterations finished qdiffx linear iterations at : 08:11:34 total time elapsed so far: 21.17000 # loops : 180 mean,max change (kT/e) : 1.2018869E-03 2.0996094E-02 energy calculations done at 21.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.35000 DelPhi exited at 08:11:34 21.357u 0.484s 0:22.77 95.8% 0+0k 0+0io 0pf+0w