Mon Oct 10 16:19:13 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 Mon Oct 10 2011 at 16:19:13 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 = 2396 !!! WARNING: GLU 347 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6198096 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): 201.8300 259.0080 ymin,ymax (A): 59.16400 105.8440 zmin,zma (A): 157.6250 215.0620 x,y,z range (A): 57.17799 46.68000 57.43700 scale (grids/A): 0.6198096 object centre (A): 230.4190 82.50400 186.3435 number of atom coordinates read : 2396 total number of charged atoms : 2259 net assigned charge : 9.728023 assigned positive charge : 359.5859 centred at (gu) : 90.15871 91.54456 91.33801 assigned negative charge : -349.8586 centred at (gu) : 90.28941 91.59867 91.42505 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6269 nv = 96 ne = 84 npr = 46602 no. pairs analyzed = 46602 no. exposed pairs = 3260 no. arc points = 23762 no. surface atoms = 1093 nbur = 1303 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 3064 m= 0 mr = 30 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2472 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7624 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7534611E-09 3.4816199E-09 midg,1,midg; midg,igrid,midg 7.9684765E-09 6.4397652E-09 1,midg,midg; igrid,midg,midg 1.5014034E-08 2.9938961E-11 gauss-seidel spectral radius is 0.9865140 estimated iterations to convergence 70 setup time was (sec) 0.3600000 now iterating at: 16:19:13 rms-change max change #iterations 0.1172424 16.96866 at 10iterations 1.0377519E-02 1.482615 at 20iterations 9.4819168E-04 0.1530094 at 30iterations 8.8202039E-05 1.7148018E-02 at 40iterations 8.0992813E-06 1.2550354E-03 at 50iterations finished qdiffx linear iterations at : 16:19:16 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 8.0992813E-06 1.2550354E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 16:19:17 3.343u 0.183s 0:03.81 92.3% 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 Mon Oct 10 2011 at 16:19:17 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 = 2396 !!! WARNING: GLU 347 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.859429 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): 201.8300 259.0080 ymin,ymax (A): 59.16400 105.8440 zmin,zma (A): 157.6250 215.0620 x,y,z range (A): 57.17799 46.68000 57.43700 scale (grids/A): 1.859429 object centre (A): 230.4190 82.50400 186.3435 number of atom coordinates read : 2396 total number of charged atoms : 2259 net assigned charge : 9.728023 assigned positive charge : 359.5859 centred at (gu) : 90.47546 94.63317 94.01359 assigned negative charge : -349.8586 centred at (gu) : 90.86790 94.79575 94.27499 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23762 grid for indexing accessible points = 1.400000 m= 22347 mr = 42353 m= 2943 mr = 15642 m= 142 mr = 1587 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 443 time to turn everything in is 0.3200000 number of dielectric boundary points 32190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 17743 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) : 0.6198096 object centre at (A) : 230.4190 82.50400 186.3435 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6211733E-04 7.1766532E-05 midg,1,midg; midg,igrid,midg 1.3941202E-02 1.8950831E-02 1,midg,midg; igrid,midg,midg 2.5363371E-02 -1.4583704E-03 gauss-seidel spectral radius is 0.9985586 estimated iterations to convergence 209 setup time was (sec) 0.5400000 now iterating at: 16:19:17 rms-change max change #iterations 3.785879 168.0730 at 10iterations 1.721611 66.38918 at 20iterations 0.7868139 31.80675 at 30iterations 0.3597113 12.20036 at 40iterations 0.1641450 5.958372 at 50iterations 7.5097606E-02 2.370171 at 60iterations 3.4209400E-02 1.141930 at 70iterations 1.5643993E-02 0.5004959 at 80iterations 7.1623260E-03 0.2339287 at 90iterations 3.2724023E-03 0.1126575 at 100iterations 1.5038721E-03 4.8971772E-02 at 110iterations 6.8679667E-04 2.3534775E-02 at 120iterations finished qdiffx linear iterations at : 16:19:24 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 6.8679667E-04 2.3534775E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 16:19:25 7.618u 0.187s 0:08.10 96.1% 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 16:19:25 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 = 2396 !!! WARNING: GLU 347 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.789143 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): 201.8300 259.0080 ymin,ymax (A): 59.16400 105.8440 zmin,zma (A): 157.6250 215.0620 x,y,z range (A): 57.17799 46.68000 57.43700 scale (grids/A): 2.789143 object centre (A): 230.4190 82.50400 186.3435 number of atom coordinates read : 2396 total number of charged atoms : 2259 net assigned charge : 9.728023 assigned positive charge : 359.5859 centred at (gu) : 90.71313 96.94958 96.02026 assigned negative charge : -349.8586 centred at (gu) : 91.30180 97.19360 96.41243 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 152958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23762 grid for indexing accessible points = 1.400000 m= 72289 mr = 103193 m= 24727 mr = 56990 m= 5005 mr = 19194 m= 523 mr = 3432 m= 28 mr = 266 m= 0 mr = 14 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 1420 time to turn everything in is 0.8200000 number of dielectric boundary points 72441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 18065 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) : 1.859429 object centre at (A) : 230.4190 82.50400 186.3435 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6458906 -3.7215095E-02 midg,1,midg; midg,igrid,midg 0.1079542 0.1810457 1,midg,midg; igrid,midg,midg 0.1746312 2.6867639E-02 gauss-seidel spectral radius is 0.9992467 estimated iterations to convergence 288 setup time was (sec) 1.050000 now iterating at: 16:19:26 rms-change max change #iterations 9.173043 364.1633 at 10iterations 5.383107 127.1653 at 20iterations 3.113951 73.17789 at 30iterations 1.800192 36.99318 at 40iterations 1.036674 27.86960 at 50iterations 0.5936713 12.04357 at 60iterations 0.3404526 7.633735 at 70iterations 0.1947214 4.126944 at 80iterations 0.1116569 2.404152 at 90iterations 6.3940018E-02 1.263084 at 100iterations 3.6448095E-02 0.7858765 at 110iterations 2.0821052E-02 0.4104996 at 120iterations 1.1848884E-02 0.2499161 at 130iterations 6.7867795E-03 0.1378479 at 140iterations 3.8746893E-03 7.2856903E-02 at 150iterations 2.2108916E-03 4.7484398E-02 at 160iterations 1.2612273E-03 2.4318695E-02 at 170iterations 7.1933225E-04 1.5480042E-02 at 180iterations finished qdiffx linear iterations at : 16:19:37 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 7.1933225E-04 1.5480042E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 16:19:38 12.366u 0.217s 0:12.86 97.7% 0+0k 0+0io 0pf+0w