Mon Oct 10 16:04:05 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 16:04:05 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5172 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4728070 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): 7.533000 62.66700 ymin,ymax (A): -28.87200 46.42300 zmin,zma (A): -29.12700 33.62900 x,y,z range (A): 55.13400 75.29500 62.75600 scale (grids/A): 0.4728070 object centre (A): 35.10000 8.775500 2.251000 number of atom coordinates read : 5172 total number of charged atoms : 5007 net assigned charge : 3.920032 assigned positive charge : 780.4174 centred at (gu) : 89.61896 88.97012 89.21519 assigned negative charge : -776.5023 centred at (gu) : 89.61256 88.95892 89.23076 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7002 nv = 96 ne = 84 npr = 106435 no. pairs analyzed = 106435 no. exposed pairs = 6227 no. arc points = 41720 no. surface atoms = 2111 nbur = 3061 mkacc time = 0.1800000 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 = 1.792000 m= 196 mr = 3683 m= 0 mr = 1 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3948 ## 736 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9667 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0788600E-11 1.1334896E-12 midg,1,midg; midg,igrid,midg 4.5643454E-12 1.0896705E-11 1,midg,midg; igrid,midg,midg 6.5005462E-12 1.0935386E-11 gauss-seidel spectral radius is 0.9771629 estimated iterations to convergence 55 setup time was (sec) 0.5400000 now iterating at: 16:04:05 rms-change max change #iterations 4.8084203E-02 8.259998 at 10iterations 3.4759776E-03 0.5828819 at 20iterations 1.1012072E-03 0.1552734 at 30iterations 4.5537154E-04 6.1433792E-02 at 40iterations 1.9171517E-04 2.6715279E-02 at 50iterations finished qdiffx linear iterations at : 16:04:08 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 1.9171517E-04 2.6715279E-02 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 16:04:09 3.647u 0.170s 0:04.10 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 Mon Oct 10 2011 at 16:04:09 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5172 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 1.418421 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): 7.533000 62.66700 ymin,ymax (A): -28.87200 46.42300 zmin,zma (A): -29.12700 33.62900 x,y,z range (A): 55.13400 75.29500 62.75600 scale (grids/A): 1.418421 object centre (A): 35.10000 8.775500 2.251000 number of atom coordinates read : 5172 total number of charged atoms : 5007 net assigned charge : 3.920032 assigned positive charge : 780.4174 centred at (gu) : 88.85506 86.90875 87.64434 assigned negative charge : -776.5023 centred at (gu) : 88.83739 86.87634 87.69172 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 81664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41720 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 21638 mr = 57337 m= 1435 mr = 14063 m= 21 mr = 505 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 801 time to turn everything in is 0.4100000 number of dielectric boundary points 32853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 731 ## 20 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 36489 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) : 0.4728070 object centre at (A) : 35.10000 8.775500 2.251000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1198430E-04 -4.9023242E-03 midg,1,midg; midg,igrid,midg 1.5871493E-02 1.2178721E-02 1,midg,midg; igrid,midg,midg 1.4403393E-03 1.6138379E-03 gauss-seidel spectral radius is 0.9977742 estimated iterations to convergence 169 setup time was (sec) 0.6100000 now iterating at: 16:04:10 rms-change max change #iterations 3.276726 130.9080 at 10iterations 1.243283 45.14334 at 20iterations 0.4732050 15.73483 at 30iterations 0.1803702 6.406631 at 40iterations 6.8558700E-02 2.745468 at 50iterations 2.6415970E-02 0.9437122 at 60iterations 1.0401998E-02 0.3906250 at 70iterations 4.4134310E-03 0.1584778 at 80iterations 2.1726734E-03 8.3916664E-02 at 90iterations 1.2935798E-03 3.8080215E-02 at 100iterations 8.8352791E-04 2.5718689E-02 at 110iterations 6.2915473E-04 1.6967773E-02 at 120iterations finished qdiffx linear iterations at : 16:04:17 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 6.2915473E-04 1.6967773E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 16:04:17 7.920u 0.214s 0:08.43 96.4% 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 Mon Oct 10 2011 at 16:04:17 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5172 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 2.127631 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): 7.533000 62.66700 ymin,ymax (A): -28.87200 46.42300 zmin,zma (A): -29.12700 33.62900 x,y,z range (A): 55.13400 75.29500 62.75600 scale (grids/A): 2.127631 object centre (A): 35.10000 8.775500 2.251000 number of atom coordinates read : 5172 total number of charged atoms : 5007 net assigned charge : 3.920032 assigned positive charge : 780.4174 centred at (gu) : 88.28223 85.36273 86.46624 assigned negative charge : -776.5023 centred at (gu) : 88.25591 85.31453 86.53746 start vw surface at 0.1400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 191420 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41720 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 81004 mr = 141624 m= 17578 mr = 62630 m= 1795 mr = 12311 m= 43 mr = 940 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2656 time to turn everything in is 0.9700000 number of dielectric boundary points 74327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 39782 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) : 1.418421 object centre at (A) : 35.10000 8.775500 2.251000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9683087E-02 -0.1163295 midg,1,midg; midg,igrid,midg 0.4164435 0.5017899 1,midg,midg; igrid,midg,midg 5.1067442E-02 5.0015207E-02 gauss-seidel spectral radius is 0.9990602 estimated iterations to convergence 258 setup time was (sec) 1.210000 now iterating at: 16:04:19 rms-change max change #iterations 9.356969 349.2809 at 10iterations 5.180165 125.7407 at 20iterations 2.841797 65.97485 at 30iterations 1.554773 36.74034 at 40iterations 0.8467540 18.00810 at 50iterations 0.4587017 11.00417 at 60iterations 0.2479943 5.006750 at 70iterations 0.1337993 2.895846 at 80iterations 7.2120383E-02 1.451805 at 90iterations 3.8965747E-02 0.7492008 at 100iterations 2.1035822E-02 0.4829066 at 110iterations 1.1356876E-02 0.2442493 at 120iterations 6.1824787E-03 0.1380577 at 130iterations 3.4106323E-03 7.5178146E-02 at 140iterations 1.9392719E-03 3.9920330E-02 at 150iterations 1.1635871E-03 2.5161743E-02 at 160iterations 7.5031299E-04 1.4251709E-02 at 170iterations 5.2238797E-04 9.6759796E-03 at 180iterations finished qdiffx linear iterations at : 16:04:30 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 5.2238797E-04 9.6759796E-03 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 16:04:31 12.850u 0.207s 0:13.33 97.8% 0+0k 0+0io 0pf+0w