Tue Oct 11 08:05:49 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 Tue Oct 11 2011 at 08:05:49 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2404 !!! WARNING: WAT 3 has a net charge of -0.8340 !!! WARNING: WAT 4 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6147045 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): -16.89100 27.93100 ymin,ymax (A): 13.48600 71.40000 zmin,zma (A): -13.31200 38.42300 x,y,z range (A): 44.82200 57.91400 51.73500 scale (grids/A): 0.6147045 object centre (A): 5.520000 42.44300 12.55550 number of atom coordinates read : 2404 total number of charged atoms : 2259 net assigned charge : 7.332023 assigned positive charge : 349.8389 centred at (gu) : 89.33918 90.02482 90.85059 assigned negative charge : -342.5078 centred at (gu) : 89.28322 90.11906 90.77341 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6149 nv = 96 ne = 84 npr = 47831 no. pairs analyzed = 47831 no. exposed pairs = 3174 no. arc points = 22846 no. surface atoms = 1065 nbur = 1339 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 3152 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3500000 number of dielectric boundary points 3310 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2298 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7492 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.4251340E-10 1.0666989E-08 midg,1,midg; midg,igrid,midg 9.6285744E-09 2.1700217E-10 1,midg,midg; igrid,midg,midg 2.4783593E-09 6.7472326E-09 gauss-seidel spectral radius is 0.9862883 estimated iterations to convergence 70 setup time was (sec) 0.6200000 now iterating at: 08:05:50 rms-change max change #iterations 0.1161985 19.13098 at 10iterations 1.0307648E-02 1.387598 at 20iterations 9.0450404E-04 0.1497221 at 30iterations 8.2667990E-05 1.1576176E-02 at 40iterations 7.3800106E-06 1.3008118E-03 at 50iterations finished qdiffx linear iterations at : 08:05:53 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 7.3800106E-06 1.3008118E-03 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 08:05:54 4.008u 0.194s 0:04.79 87.4% 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 Tue Oct 11 2011 at 08:05:54 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2404 !!! WARNING: WAT 3 has a net charge of -0.8340 !!! WARNING: WAT 4 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.844114 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): -16.89100 27.93100 ymin,ymax (A): 13.48600 71.40000 zmin,zma (A): -13.31200 38.42300 x,y,z range (A): 44.82200 57.91400 51.73500 scale (grids/A): 1.844114 object centre (A): 5.520000 42.44300 12.55550 number of atom coordinates read : 2404 total number of charged atoms : 2259 net assigned charge : 7.332023 assigned positive charge : 349.8389 centred at (gu) : 88.01702 90.07389 92.55124 assigned negative charge : -342.5078 centred at (gu) : 87.84955 90.35700 92.32006 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 66734 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22846 grid for indexing accessible points = 1.400000 m= 22374 mr = 44427 m= 3047 mr = 15630 m= 147 mr = 1676 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 472 time to turn everything in is 0.6100000 number of dielectric boundary points 30525 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17679 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) : 0.6147045 object centre at (A) : 5.520000 42.44300 12.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5763462E-03 1.8080389E-02 midg,1,midg; midg,igrid,midg 4.0279206E-02 -1.6276600E-02 1,midg,midg; igrid,midg,midg 9.4363317E-03 1.1101207E-02 gauss-seidel spectral radius is 0.9985310 estimated iterations to convergence 207 setup time was (sec) 0.9500000 now iterating at: 08:05:55 rms-change max change #iterations 3.684537 171.0851 at 10iterations 1.669109 66.12158 at 20iterations 0.7627766 25.40476 at 30iterations 0.3453454 14.23405 at 40iterations 0.1570347 5.707027 at 50iterations 7.1136206E-02 2.603880 at 60iterations 3.2385178E-02 1.137105 at 70iterations 1.4686625E-02 0.4779811 at 80iterations 6.6696787E-03 0.2168732 at 90iterations 3.0444227E-03 0.1087341 at 100iterations 1.3776922E-03 4.7500610E-02 at 110iterations 6.2947633E-04 2.1121264E-02 at 120iterations finished qdiffx linear iterations at : 08:06:03 total time elapsed so far: 8.640000 # loops : 120 mean,max change (kT/e) : 6.2947633E-04 2.1121264E-02 energy calculations done at 8.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.870000 DelPhi exited at 08:06:03 8.877u 0.203s 0:09.46 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 Tue Oct 11 2011 at 08:06:04 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2404 !!! WARNING: WAT 3 has a net charge of -0.8340 !!! WARNING: WAT 4 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.766171 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): -16.89100 27.93100 ymin,ymax (A): 13.48600 71.40000 zmin,zma (A): -13.31200 38.42300 x,y,z range (A): 44.82200 57.91400 51.73500 scale (grids/A): 2.766171 object centre (A): 5.520000 42.44300 12.55550 number of atom coordinates read : 2404 total number of charged atoms : 2259 net assigned charge : 7.332023 assigned positive charge : 349.8389 centred at (gu) : 87.02528 90.11067 93.82672 assigned negative charge : -342.5078 centred at (gu) : 86.77443 90.53554 93.48011 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 154511 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22846 grid for indexing accessible points = 1.400000 m= 73378 mr = 108523 m= 24751 mr = 58264 m= 5136 mr = 18948 m= 668 mr = 3581 m= 22 mr = 412 m= 0 mr = 10 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 1451 time to turn everything in is 1.470000 number of dielectric boundary points 68728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 18069 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) : 1.844114 object centre at (A) : 5.520000 42.44300 12.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6597969E-02 0.2066169 midg,1,midg; midg,igrid,midg 0.6160814 -0.4458323 1,midg,midg; igrid,midg,midg 0.1329886 0.1166255 gauss-seidel spectral radius is 0.9992342 estimated iterations to convergence 285 setup time was (sec) 1.830000 now iterating at: 08:06:06 rms-change max change #iterations 9.054157 327.2905 at 10iterations 5.312274 137.0383 at 20iterations 3.083593 83.44150 at 30iterations 1.776971 41.80396 at 40iterations 1.021615 21.44369 at 50iterations 0.5840191 13.30325 at 60iterations 0.3336886 7.539799 at 70iterations 0.1908018 3.769570 at 80iterations 0.1085630 2.341400 at 90iterations 6.1976064E-02 1.203379 at 100iterations 3.5244986E-02 0.7151299 at 110iterations 2.0044481E-02 0.4174900 at 120iterations 1.1418702E-02 0.2380939 at 130iterations 6.4992961E-03 0.1313324 at 140iterations 3.7028007E-03 7.7941895E-02 at 150iterations 2.1020568E-03 4.2850494E-02 at 160iterations 1.1962467E-03 2.4890900E-02 at 170iterations 6.7966938E-04 1.2399673E-02 at 180iterations finished qdiffx linear iterations at : 08:06:18 total time elapsed so far: 13.89000 # loops : 180 mean,max change (kT/e) : 6.7966938E-04 1.2399673E-02 energy calculations done at 13.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.12000 DelPhi exited at 08:06:18 14.123u 0.205s 0:14.65 97.7% 0+0k 0+0io 0pf+0w