Mon Oct 10 17:09:34 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 Mon Oct 10 2011 at 17:09:34 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2641 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 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: 0.6090989 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): -9.342999 49.10400 ymin,ymax (A): 3.734000 53.41900 zmin,zma (A): 6.187000 61.02300 x,y,z range (A): 58.44700 49.68500 54.83600 scale (grids/A): 0.6090989 object centre (A): 19.88050 28.57650 33.60500 number of atom coordinates read : 2641 total number of charged atoms : 2501 net assigned charge : -2.257974 assigned positive charge : 399.9365 centred at (gu) : 88.51014 89.99211 90.90290 assigned negative charge : -402.1955 centred at (gu) : 88.38546 90.13936 90.93655 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6810 nv = 96 ne = 84 npr = 50761 no. pairs analyzed = 50761 no. exposed pairs = 3856 no. arc points = 27269 no. surface atoms = 1292 nbur = 1349 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 3260 m= 0 mr = 28 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2737 ## 279 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8187 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0119741E-10 -3.4781626E-09 midg,1,midg; midg,igrid,midg 6.0523893E-09 -8.5942569E-09 1,midg,midg; igrid,midg,midg -1.0472142E-08 3.5215679E-09 gauss-seidel spectral radius is 0.9860646 estimated iterations to convergence 69 setup time was (sec) 0.3900000 now iterating at: 17:09:34 rms-change max change #iterations 0.1157262 17.90251 at 10iterations 1.0146897E-02 1.550392 at 20iterations 8.7761204E-04 0.1324968 at 30iterations 7.8508245E-05 1.1526108E-02 at 40iterations 7.4819304E-06 1.0776520E-03 at 50iterations finished qdiffx linear iterations at : 17:09:37 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 7.4819304E-06 1.0776520E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 17:09:38 3.373u 0.170s 0:03.89 91.0% 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 17:09:38 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2641 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 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: 1.827297 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): -9.342999 49.10400 ymin,ymax (A): 3.734000 53.41900 zmin,zma (A): 6.187000 61.02300 x,y,z range (A): 58.44700 49.68500 54.83600 scale (grids/A): 1.827297 object centre (A): 19.88050 28.57650 33.60500 number of atom coordinates read : 2641 total number of charged atoms : 2501 net assigned charge : -2.257974 assigned positive charge : 399.9365 centred at (gu) : 85.52975 89.97570 92.70790 assigned negative charge : -402.1955 centred at (gu) : 85.15598 90.41773 92.80962 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27269 grid for indexing accessible points = 1.400000 m= 24506 mr = 46556 m= 3321 mr = 16613 m= 142 mr = 1807 m= 0 mr = 26 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 35366 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19597 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) : 0.6090989 object centre at (A) : 19.88050 28.57650 33.60500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0012571E-03 5.3897696E-03 midg,1,midg; midg,igrid,midg 1.0025736E-02 -2.4543298E-02 1,midg,midg; igrid,midg,midg -5.6353204E-02 2.7325960E-02 gauss-seidel spectral radius is 0.9985469 estimated iterations to convergence 208 setup time was (sec) 0.5700000 now iterating at: 17:09:38 rms-change max change #iterations 4.004100 182.6115 at 10iterations 1.822113 65.83302 at 20iterations 0.8285891 28.71211 at 30iterations 0.3762174 13.96380 at 40iterations 0.1712951 5.882538 at 50iterations 7.7999406E-02 2.641629 at 60iterations 3.5502438E-02 1.169164 at 70iterations 1.6224436E-02 0.5613718 at 80iterations 7.4110543E-03 0.2482781 at 90iterations 3.3740862E-03 0.1172142 at 100iterations 1.5430623E-03 4.8065186E-02 at 110iterations 7.0551928E-04 2.2524357E-02 at 120iterations finished qdiffx linear iterations at : 17:09:46 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 7.0551928E-04 2.2524357E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 17:09:46 7.727u 0.190s 0:08.30 95.3% 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 17:09:46 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2641 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 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: 2.740945 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): -9.342999 49.10400 ymin,ymax (A): 3.734000 53.41900 zmin,zma (A): 6.187000 61.02300 x,y,z range (A): 58.44700 49.68500 54.83600 scale (grids/A): 2.740945 object centre (A): 19.88050 28.57650 33.60500 number of atom coordinates read : 2641 total number of charged atoms : 2501 net assigned charge : -2.257974 assigned positive charge : 399.9365 centred at (gu) : 83.29443 89.96336 94.06155 assigned negative charge : -402.1955 centred at (gu) : 82.73399 90.62664 94.21429 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 167066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27269 grid for indexing accessible points = 1.400000 m= 79618 mr = 113907 m= 26800 mr = 61640 m= 5706 mr = 20230 m= 606 mr = 3930 m= 18 mr = 328 m= 0 mr = 3 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8900000 number of dielectric boundary points 79776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 20007 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) : 1.827297 object centre at (A) : 19.88050 28.57650 33.60500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2405173 0.2166338 midg,1,midg; midg,igrid,midg 9.4426930E-02 -0.2218268 1,midg,midg; igrid,midg,midg -0.7320552 0.2980886 gauss-seidel spectral radius is 0.9992585 estimated iterations to convergence 290 setup time was (sec) 1.130000 now iterating at: 17:09:47 rms-change max change #iterations 9.919218 349.7971 at 10iterations 5.906720 150.2204 at 20iterations 3.478733 103.9477 at 30iterations 2.023473 42.00224 at 40iterations 1.176706 25.87132 at 50iterations 0.6808878 12.48706 at 60iterations 0.3940036 8.265009 at 70iterations 0.2267023 4.265111 at 80iterations 0.1305723 2.742215 at 90iterations 7.5315312E-02 1.527668 at 100iterations 4.3248069E-02 0.8049459 at 110iterations 2.4852889E-02 0.5252581 at 120iterations 1.4262250E-02 0.2704067 at 130iterations 8.1748646E-03 0.1570129 at 140iterations 4.7007017E-03 8.5548401E-02 at 150iterations 2.6981523E-03 4.9623489E-02 at 160iterations 1.5497116E-03 2.9550791E-02 at 170iterations 8.8753109E-04 1.5995026E-02 at 180iterations finished qdiffx linear iterations at : 17:09:59 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 8.8753109E-04 1.5995026E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 17:09:59 12.534u 0.204s 0:13.24 96.1% 0+0k 0+0io 0pf+0w