Sat Oct 8 15:17:21 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 Sat Oct 8 2011 at 15:17:21 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIT 207 has a net charge of 0.5140 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: 0.6027360 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 : 2.014010 assigned positive charge : 426.3114 centred at (gu) : 90.57158 89.40124 89.86369 assigned negative charge : -424.2984 centred at (gu) : 90.60801 89.39663 89.86466 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 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 = 0.1500000 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 = 0.1900000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3400000 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 1.0262475E-09 8.8514285E-10 midg,1,midg; midg,igrid,midg 8.5801566E-10 1.0114289E-09 1,midg,midg; igrid,midg,midg 2.2230811E-09 -7.3076611E-10 gauss-seidel spectral radius is 0.9857702 estimated iterations to convergence 69 setup time was (sec) 0.6500000 now iterating at: 15:17:22 rms-change max change #iterations 0.1145033 17.24586 at 10iterations 1.0213762E-02 1.386961 at 20iterations 1.0751701E-03 0.1534538 at 30iterations 1.7847310E-04 2.5264740E-02 at 40iterations 4.3556091E-05 6.0920715E-03 at 50iterations finished qdiffx linear iterations at : 15:17:27 total time elapsed so far: 5.190000 # loops : 50 mean,max change (kT/e) : 4.3556091E-05 6.0920715E-03 energy calculations done at 5.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.350000 DelPhi exited at 15:17:27 5.356u 0.485s 0:06.08 95.8% 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 15:17:27 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIT 207 has a net charge of 0.5140 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 : 2.014010 assigned positive charge : 426.3114 centred at (gu) : 91.71422 88.20315 89.59046 assigned negative charge : -424.2984 centred at (gu) : 91.82379 88.18965 89.59376 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 = 0.3300000 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 0.7600000 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 -2.0160829E-03 -1.5107676E-02 midg,1,midg; midg,igrid,midg 2.4883221E-03 6.5953243E-03 1,midg,midg; igrid,midg,midg 3.5393622E-02 1.4138929E-02 gauss-seidel spectral radius is 0.9985111 estimated iterations to convergence 206 setup time was (sec) 0.9700000 now iterating at: 15:17:28 rms-change max change #iterations 4.004122 172.5076 at 10iterations 1.804246 59.39687 at 20iterations 0.8209704 28.47872 at 30iterations 0.3697683 12.41240 at 40iterations 0.1682847 5.588280 at 50iterations 7.6213732E-02 2.514048 at 60iterations 3.4532454E-02 1.218014 at 70iterations 1.5703371E-02 0.5862255 at 80iterations 7.1482272E-03 0.2191672 at 90iterations 3.2612672E-03 0.1030350 at 100iterations 1.4964675E-03 4.9926758E-02 at 110iterations 6.9280108E-04 2.4322510E-02 at 120iterations finished qdiffx linear iterations at : 15:17:40 total time elapsed so far: 12.56000 # loops : 120 mean,max change (kT/e) : 6.9280108E-04 2.4322510E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 15:17:41 12.747u 0.545s 0:13.58 97.7% 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 15:17:41 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIT 207 has a net charge of 0.5140 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 : 2.014010 assigned positive charge : 426.3114 centred at (gu) : 92.57111 87.30451 89.38536 assigned negative charge : -424.2984 centred at (gu) : 92.73558 87.28436 89.39063 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 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 = 1.030000 no. cavity mid-points inaccessible to solvent = 559 time to turn everything in is 1.670000 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 1.840000 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 -8.7846769E-05 -0.2016606 midg,1,midg; midg,igrid,midg -3.0632152E-03 7.8118727E-02 1,midg,midg; igrid,midg,midg 0.4051401 0.2579888 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 2.070000 now iterating at: 15:17:43 rms-change max change #iterations 9.655874 341.6830 at 10iterations 5.551658 131.1953 at 20iterations 3.187035 70.45293 at 30iterations 1.823782 36.91367 at 40iterations 1.042601 21.00589 at 50iterations 0.5951663 11.94692 at 60iterations 0.3387974 6.176881 at 70iterations 0.1935198 3.796314 at 80iterations 0.1098153 1.854165 at 90iterations 6.2509194E-02 1.267240 at 100iterations 3.5569124E-02 0.6751156 at 110iterations 2.0270200E-02 0.3847094 at 120iterations 1.1528584E-02 0.2184486 at 130iterations 6.6015078E-03 0.1203136 at 140iterations 3.7697316E-03 6.8854332E-02 at 150iterations 2.1715171E-03 4.2226791E-02 at 160iterations 1.2572574E-03 2.8108597E-02 at 170iterations 7.4023055E-04 1.2752533E-02 at 180iterations finished qdiffx linear iterations at : 15:18:03 total time elapsed so far: 21.40000 # loops : 180 mean,max change (kT/e) : 7.4023055E-04 1.2752533E-02 energy calculations done at 21.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.57000 DelPhi exited at 15:18:03 21.573u 0.555s 0:22.40 98.7% 0+0k 0+0io 0pf+0w