Sat Oct 8 15:16:39 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 Sat Oct 8 2011 at 15:16:39 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6027360 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): -0.6589999 58.40500 ymin,ymax (A): -24.07600 26.83300 zmin,zma (A): -10.12800 43.21500 x,y,z range (A): 59.06400 50.90900 53.34300 scale (grids/A): 0.6027360 object centre (A): 28.87300 1.378500 16.54350 number of atom coordinates read : 2859 total number of charged atoms : 2716 net assigned charge : 2.000010 assigned positive charge : 424.2693 centred at (gu) : 90.60782 89.40936 89.88536 assigned negative charge : -422.2704 centred at (gu) : 90.64381 89.40415 89.88523 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6839 nv = 96 ne = 84 npr = 59258 no. pairs analyzed = 59258 no. exposed pairs = 3401 no. arc points = 23304 no. surface atoms = 1156 nbur = 1703 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 = 1.456000 m= 329 mr = 3846 m= 0 mr = 27 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3500000 number of dielectric boundary points 3295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2394 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8572 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6634201E-10 9.2993890E-10 midg,1,midg; midg,igrid,midg 8.2143620E-10 1.0296564E-09 1,midg,midg; igrid,midg,midg 2.1768933E-09 -7.1320672E-10 gauss-seidel spectral radius is 0.9857702 estimated iterations to convergence 69 setup time was (sec) 0.6600000 now iterating at: 15:16:40 rms-change max change #iterations 0.1132350 17.24586 at 10iterations 1.0081603E-02 1.419273 at 20iterations 1.0634745E-03 0.1466293 at 30iterations 1.7622321E-04 2.4782181E-02 at 40iterations 4.2999163E-05 6.0081482E-03 at 50iterations finished qdiffx linear iterations at : 15:16:44 total time elapsed so far: 5.130000 # loops : 50 mean,max change (kT/e) : 4.2999163E-05 6.0081482E-03 energy calculations done at 5.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.310000 DelPhi exited at 15:16:45 5.319u 0.464s 0:06.09 94.7% 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 Sat Oct 8 2011 at 15:16:45 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.808208 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): -0.6589999 58.40500 ymin,ymax (A): -24.07600 26.83300 zmin,zma (A): -10.12800 43.21500 x,y,z range (A): 59.06400 50.90900 53.34300 scale (grids/A): 1.808208 object centre (A): 28.87300 1.378500 16.54350 number of atom coordinates read : 2859 total number of charged atoms : 2716 net assigned charge : 2.000010 assigned positive charge : 424.2693 centred at (gu) : 91.82291 88.22743 89.65545 assigned negative charge : -422.2704 centred at (gu) : 91.93115 88.21224 89.65547 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23304 grid for indexing accessible points = 1.400000 m= 25651 mr = 53660 m= 3345 mr = 18612 m= 131 mr = 1892 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 176 time to turn everything in is 0.6300000 number of dielectric boundary points 30444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 21210 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) : 0.6027360 object centre at (A) : 28.87300 1.378500 16.54350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9144516E-03 -1.5083987E-02 midg,1,midg; midg,igrid,midg 2.5661229E-03 6.5578609E-03 1,midg,midg; igrid,midg,midg 3.5922520E-02 1.4125283E-02 gauss-seidel spectral radius is 0.9985111 estimated iterations to convergence 206 setup time was (sec) 0.9600000 now iterating at: 15:16:46 rms-change max change #iterations 3.982440 172.5076 at 10iterations 1.793694 59.39590 at 20iterations 0.8164690 27.78186 at 30iterations 0.3677835 12.43182 at 40iterations 0.1673006 5.668296 at 50iterations 7.5756274E-02 2.411084 at 60iterations 3.4342974E-02 1.204317 at 70iterations 1.5615759E-02 0.5829906 at 80iterations 7.1079545E-03 0.2159753 at 90iterations 3.2427879E-03 0.1039734 at 100iterations 1.4871377E-03 4.8183441E-02 at 110iterations 6.8829168E-04 2.3864746E-02 at 120iterations finished qdiffx linear iterations at : 15:16:58 total time elapsed so far: 12.33000 # loops : 120 mean,max change (kT/e) : 6.8829168E-04 2.3864746E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.50000 DelPhi exited at 15:16:58 12.506u 0.565s 0:13.37 97.6% 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 8 2011 at 15:16:58 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.712312 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): -0.6589999 58.40500 ymin,ymax (A): -24.07600 26.83300 zmin,zma (A): -10.12800 43.21500 x,y,z range (A): 59.06400 50.90900 53.34300 scale (grids/A): 2.712312 object centre (A): 28.87300 1.378500 16.54350 number of atom coordinates read : 2859 total number of charged atoms : 2716 net assigned charge : 2.000010 assigned positive charge : 424.2693 centred at (gu) : 92.73417 87.34094 89.48283 assigned negative charge : -422.2704 centred at (gu) : 92.89661 87.31827 89.48324 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 174916 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23304 grid for indexing accessible points = 1.400000 m= 86205 mr = 129926 m= 28100 mr = 70349 m= 5700 mr = 21999 m= 529 mr = 4153 m= 8 mr = 270 m= 0 mr = 2 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 559 time to turn everything in is 1.660000 number of dielectric boundary points 68759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 21726 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) : 1.808208 object centre at (A) : 28.87300 1.378500 16.54350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4248920E-03 -0.2015628 midg,1,midg; midg,igrid,midg -2.2849038E-03 7.7554129E-02 1,midg,midg; igrid,midg,midg 0.4156553 0.2577822 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 2.040000 now iterating at: 15:17:01 rms-change max change #iterations 9.603118 341.6830 at 10iterations 5.521710 131.1928 at 20iterations 3.170402 69.37262 at 30iterations 1.814575 36.52468 at 40iterations 1.037116 20.80039 at 50iterations 0.5922799 11.72802 at 60iterations 0.3371954 6.207561 at 70iterations 0.1925742 3.823412 at 80iterations 0.1092851 1.827925 at 90iterations 6.2214192E-02 1.256657 at 100iterations 3.5403881E-02 0.6688976 at 110iterations 2.0175999E-02 0.3806629 at 120iterations 1.1475756E-02 0.2157173 at 130iterations 6.5705422E-03 0.1203175 at 140iterations 3.7519066E-03 6.8927765E-02 at 150iterations 2.1604637E-03 4.1604996E-02 at 160iterations 1.2501206E-03 2.7895927E-02 at 170iterations 7.3553569E-04 1.2725830E-02 at 180iterations finished qdiffx linear iterations at : 15:17:20 total time elapsed so far: 21.26000 # loops : 180 mean,max change (kT/e) : 7.3553569E-04 1.2725830E-02 energy calculations done at 21.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.43000 DelPhi exited at 15:17:21 21.435u 0.607s 0:22.31 98.7% 0+0k 0+0io 0pf+0w