Sun Oct 9 06:41:40 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+sph.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 = amb.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 06:41:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: ASP 372 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5854396 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): -27.99100 32.81800 ymin,ymax (A): -0.8860000 57.69800 zmin,zma (A): -27.21600 29.08000 x,y,z range (A): 60.80900 58.58400 56.29600 scale (grids/A): 0.5854396 object centre (A): 2.413500 28.40600 0.9320002 number of atom coordinates read : 2463 total number of charged atoms : 2319 net assigned charge : -1.999984 assigned positive charge : 364.7051 centred at (gu) : 90.72284 89.45029 90.45722 assigned negative charge : -366.7057 centred at (gu) : 90.74944 89.33471 90.43381 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5827 nv = 96 ne = 84 npr = 47686 no. pairs analyzed = 47686 no. exposed pairs = 3607 no. arc points = 26816 no. surface atoms = 1211 nbur = 1252 mkacc time = 0.1100000 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 = 1.456000 m= 251 mr = 2642 m= 1 mr = 10 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 0.2700000 number of dielectric boundary points 3427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2758 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7252 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.1579461E-10 2.1078781E-12 midg,1,midg; midg,igrid,midg -3.4719523E-09 1.7248738E-09 1,midg,midg; igrid,midg,midg 5.3444124E-11 -1.2850642E-09 gauss-seidel spectral radius is 0.9849135 estimated iterations to convergence 67 setup time was (sec) 0.5300000 now iterating at: 06:41:41 rms-change max change #iterations 8.9805163E-02 23.15226 at 10iterations 7.2060367E-03 1.352845 at 20iterations 5.6266278E-04 9.4575882E-02 at 30iterations 4.4157310E-05 7.4262619E-03 at 40iterations 3.6703098E-06 5.8460236E-04 at 50iterations finished qdiffx linear iterations at : 06:41:44 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 3.6703098E-06 5.8460236E-04 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 06:41:45 4.110u 0.243s 0:04.64 93.7% 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 06:41:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: ASP 372 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.756319 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): -27.99100 32.81800 ymin,ymax (A): -0.8860000 57.69800 zmin,zma (A): -27.21600 29.08000 x,y,z range (A): 60.80900 58.58400 56.29600 scale (grids/A): 1.756319 object centre (A): 2.413500 28.40600 0.9320002 number of atom coordinates read : 2463 total number of charged atoms : 2319 net assigned charge : -1.999984 assigned positive charge : 364.7051 centred at (gu) : 92.16802 88.35056 91.37147 assigned negative charge : -366.7057 centred at (gu) : 92.24821 88.00404 91.30122 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 62622 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26816 grid for indexing accessible points = 1.400000 m= 19416 mr = 38856 m= 2278 mr = 12733 m= 90 mr = 1129 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 127 time to turn everything in is 0.5700000 number of dielectric boundary points 31680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 18041 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) : 0.5854396 object centre at (A) : 2.413500 28.40600 0.9320002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7324185E-02 9.5159765E-03 midg,1,midg; midg,igrid,midg -3.3789463E-02 -1.1987168E-03 1,midg,midg; igrid,midg,midg -1.2913459E-02 6.4692511E-03 gauss-seidel spectral radius is 0.9984097 estimated iterations to convergence 199 setup time was (sec) 0.8900000 now iterating at: 06:41:46 rms-change max change #iterations 3.486643 152.4615 at 10iterations 1.518308 59.14720 at 20iterations 0.6664345 25.86847 at 30iterations 0.2914221 11.21718 at 40iterations 0.1287853 4.905193 at 50iterations 5.6377552E-02 2.054891 at 60iterations 2.4827162E-02 1.012093 at 70iterations 1.0891620E-02 0.3966446 at 80iterations 4.8015635E-03 0.1740837 at 90iterations 2.1064689E-03 7.9371929E-02 at 100iterations 9.2516589E-04 3.5534859E-02 at 110iterations 4.0838774E-04 1.5241623E-02 at 120iterations finished qdiffx linear iterations at : 06:41:55 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 4.0838774E-04 1.5241623E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.490000 DelPhi exited at 06:41:55 9.494u 0.281s 0:10.04 97.3% 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 06:41:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: ASP 372 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.634478 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): -27.99100 32.81800 ymin,ymax (A): -0.8860000 57.69800 zmin,zma (A): -27.21600 29.08000 x,y,z range (A): 60.80900 58.58400 56.29600 scale (grids/A): 2.634478 object centre (A): 2.413500 28.40600 0.9320002 number of atom coordinates read : 2463 total number of charged atoms : 2319 net assigned charge : -1.999984 assigned positive charge : 364.7051 centred at (gu) : 93.25193 87.52573 92.05704 assigned negative charge : -366.7057 centred at (gu) : 93.37224 87.00599 91.95186 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 144704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26816 grid for indexing accessible points = 1.400000 m= 65451 mr = 95559 m= 19618 mr = 49991 m= 3697 mr = 14354 m= 337 mr = 2374 m= 9 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 429 time to turn everything in is 1.280000 number of dielectric boundary points 71395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 18538 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) : 1.756319 object centre at (A) : 2.413500 28.40600 0.9320002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3610179 0.2673177 midg,1,midg; midg,igrid,midg -0.4817394 -3.9262843E-04 1,midg,midg; igrid,midg,midg -0.2695975 0.1875268 gauss-seidel spectral radius is 0.9992099 estimated iterations to convergence 281 setup time was (sec) 1.620000 now iterating at: 06:41:57 rms-change max change #iterations 8.688611 291.6036 at 10iterations 5.050953 156.8781 at 20iterations 2.903115 93.53850 at 30iterations 1.662270 42.96494 at 40iterations 0.9478496 24.29871 at 50iterations 0.5399860 14.40855 at 60iterations 0.3061630 8.179031 at 70iterations 0.1741749 4.127674 at 80iterations 9.8469406E-02 2.216535 at 90iterations 5.5543903E-02 1.165647 at 100iterations 3.1453617E-02 0.7600346 at 110iterations 1.7715229E-02 0.3727131 at 120iterations 1.0019097E-02 0.2090340 at 130iterations 5.6416942E-03 0.1247864 at 140iterations 3.1831758E-03 6.6925049E-02 at 150iterations 1.7952196E-03 3.6603928E-02 at 160iterations 1.0121367E-03 2.1427155E-02 at 170iterations 5.6855136E-04 1.1549950E-02 at 180iterations finished qdiffx linear iterations at : 06:42:10 total time elapsed so far: 14.97000 # loops : 180 mean,max change (kT/e) : 5.6855136E-04 1.1549950E-02 energy calculations done at 14.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.14000 DelPhi exited at 06:42:11 15.145u 0.292s 0:15.71 98.2% 0+0k 0+0io 0pf+0w