Sun Oct 9 17:29:23 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 17:29:23 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 = 3351 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: 0.5227069 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): -8.670000 59.43700 ymin,ymax (A): -15.24700 34.93600 zmin,zma (A): 18.56500 71.15900 x,y,z range (A): 68.10700 50.18300 52.59400 scale (grids/A): 0.5227069 object centre (A): 25.38350 9.844499 44.86200 number of atom coordinates read : 3351 total number of charged atoms : 3204 net assigned charge : 9.000025 assigned positive charge : 516.4917 centred at (gu) : 91.23904 90.25443 89.58437 assigned negative charge : -507.4931 centred at (gu) : 91.26088 90.32354 89.54537 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5864 nv = 96 ne = 84 npr = 65857 no. pairs analyzed = 65857 no. exposed pairs = 4291 no. arc points = 29720 no. surface atoms = 1453 nbur = 1898 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 = 1.652000 m= 248 mr = 2979 m= 0 mr = 6 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3127 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2945 ## 439 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 7738 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0903007E-10 3.0306230E-10 midg,1,midg; midg,igrid,midg 4.0048920E-10 5.2902144E-12 1,midg,midg; igrid,midg,midg 2.0866334E-10 2.0583465E-10 gauss-seidel spectral radius is 0.9811756 estimated iterations to convergence 60 setup time was (sec) 0.4300000 now iterating at: 17:29:24 rms-change max change #iterations 6.2158048E-02 10.14301 at 10iterations 4.2486717E-03 0.7424698 at 20iterations 6.3249975E-04 0.1163673 at 30iterations 1.9872883E-04 2.6110649E-02 at 40iterations 8.4436324E-05 1.2169361E-02 at 50iterations finished qdiffx linear iterations at : 17:29:27 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 8.4436324E-05 1.2169361E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 17:29:27 3.513u 0.168s 0:03.95 92.9% 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 17:29:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3351 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: 1.568121 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): -8.670000 59.43700 ymin,ymax (A): -15.24700 34.93600 zmin,zma (A): 18.56500 71.15900 x,y,z range (A): 68.10700 50.18300 52.59400 scale (grids/A): 1.568121 object centre (A): 25.38350 9.844499 44.86200 number of atom coordinates read : 3351 total number of charged atoms : 3204 net assigned charge : 9.000025 assigned positive charge : 516.4917 centred at (gu) : 93.71633 90.76275 88.75219 assigned negative charge : -507.4931 centred at (gu) : 93.78235 90.97007 88.63570 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 65583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29720 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 20565 mr = 44322 m= 2187 mr = 13885 m= 45 mr = 1001 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 108 time to turn everything in is 0.3400000 number of dielectric boundary points 29172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 399 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 24222 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) : 0.5227069 object centre at (A) : 25.38350 9.844499 44.86200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1867991E-03 4.4625150E-03 midg,1,midg; midg,igrid,midg 7.2145220E-03 -3.2497675E-03 1,midg,midg; igrid,midg,midg 1.9943569E-02 1.0131148E-02 gauss-seidel spectral radius is 0.9980623 estimated iterations to convergence 181 setup time was (sec) 0.5600000 now iterating at: 17:29:28 rms-change max change #iterations 3.283236 168.3503 at 10iterations 1.329518 56.83582 at 20iterations 0.5383871 21.42997 at 30iterations 0.2189779 8.391220 at 40iterations 8.8784605E-02 3.147533 at 50iterations 3.6262885E-02 1.337281 at 60iterations 1.4828186E-02 0.6070738 at 70iterations 6.2270705E-03 0.2993631 at 80iterations 2.7319812E-03 0.1012640 at 90iterations 1.3602106E-03 5.1762104E-02 at 100iterations 8.1938348E-04 2.7579069E-02 at 110iterations 5.7701062E-04 1.8716812E-02 at 120iterations finished qdiffx linear iterations at : 17:29:35 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 5.7701062E-04 1.8716812E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 17:29:36 7.816u 0.195s 0:08.32 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 Sun Oct 9 2011 at 17:29:36 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 = 3351 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: 2.352181 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): -8.670000 59.43700 ymin,ymax (A): -15.24700 34.93600 zmin,zma (A): 18.56500 71.15900 x,y,z range (A): 68.10700 50.18300 52.59400 scale (grids/A): 2.352181 object centre (A): 25.38350 9.844499 44.86200 number of atom coordinates read : 3351 total number of charged atoms : 3204 net assigned charge : 9.000025 assigned positive charge : 516.4917 centred at (gu) : 95.57414 91.14377 88.12824 assigned negative charge : -507.4931 centred at (gu) : 95.67358 91.45494 87.95345 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 151934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29720 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 70576 mr = 108451 m= 20672 mr = 55035 m= 3355 mr = 15258 m= 193 mr = 2150 m= 0 mr = 67 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 361 time to turn everything in is 0.8100000 number of dielectric boundary points 65769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 25583 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) : 1.568121 object centre at (A) : 25.38350 9.844499 44.86200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7061600E-02 6.5803640E-02 midg,1,midg; midg,igrid,midg 0.1208698 -9.4807647E-02 1,midg,midg; igrid,midg,midg 0.6844296 -3.7569452E-02 gauss-seidel spectral radius is 0.9991072 estimated iterations to convergence 264 setup time was (sec) 1.040000 now iterating at: 17:29:37 rms-change max change #iterations 8.772231 355.6991 at 10iterations 4.911546 128.1053 at 20iterations 2.728236 71.78495 at 30iterations 1.507025 34.05339 at 40iterations 0.8325299 20.63821 at 50iterations 0.4573597 9.428509 at 60iterations 0.2508453 6.345524 at 70iterations 0.1374423 3.383290 at 80iterations 7.5297683E-02 1.606167 at 90iterations 4.1162334E-02 0.9070053 at 100iterations 2.2584798E-02 0.4826145 at 110iterations 1.2390063E-02 0.2977676 at 120iterations 6.7907772E-03 0.1478348 at 130iterations 3.7548803E-03 8.8562012E-02 at 140iterations 2.1120473E-03 5.5729866E-02 at 150iterations 1.2220888E-03 2.8359413E-02 at 160iterations 7.5234979E-04 1.7112732E-02 at 170iterations 5.0331920E-04 1.0841608E-02 at 180iterations finished qdiffx linear iterations at : 17:29:48 total time elapsed so far: 12.14000 # loops : 180 mean,max change (kT/e) : 5.0331920E-04 1.0841608E-02 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 17:29:49 12.280u 0.197s 0:12.94 96.3% 0+0k 0+0io 0pf+0w