Thu Jan 19 13:33:05 PST 2012 #!/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 Thu Jan 19 2012 at 13:33:05 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7419 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: SER 252 has a net charge of 0.2400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: LYS 737 has a net charge of 0.0200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4402399 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): 209.8200 276.2420 ymin,ymax (A): 63.29000 140.1330 zmin,zma (A): -66.93100 13.93400 x,y,z range (A): 66.42201 76.84299 80.86500 scale (grids/A): 0.4402399 object centre (A): 243.0310 101.7115 -26.49850 number of atom coordinates read : 7419 total number of charged atoms : 7172 net assigned charge : -1.707927 assigned positive charge : 1107.517 centred at (gu) : 91.02592 89.84335 89.17338 assigned negative charge : -1109.235 centred at (gu) : 91.06145 89.84082 89.08652 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8527 nv = 96 ne = 84 npr = 149925 no. pairs analyzed = 149925 no. exposed pairs = 9848 no. arc points = 64565 no. surface atoms = 3342 nbur = 4077 mkacc time = 0.2600000 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 = 1.904000 m= 257 mr = 4021 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5464 ## 1034 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 11675 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4585468E-11 7.8021981E-12 midg,1,midg; midg,igrid,midg -8.3809256E-13 -1.7185382E-13 1,midg,midg; igrid,midg,midg 2.8138318E-12 -6.6887923E-12 gauss-seidel spectral radius is 0.9738463 estimated iterations to convergence 52 setup time was (sec) 0.7100000 now iterating at: 13:33:06 rms-change max change #iterations 3.7363824E-02 5.691677 at 10iterations 2.4801602E-03 0.3639755 at 20iterations 8.1486074E-04 0.1028461 at 30iterations 3.1720023E-04 3.9354801E-02 at 40iterations 1.2425047E-04 1.5667439E-02 at 50iterations finished qdiffx linear iterations at : 13:33:10 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 1.2425047E-04 1.5667439E-02 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 13:33:10 3.938u 0.260s 0:05.82 71.9% 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 Thu Jan 19 2012 at 13:33:11 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7419 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: SER 252 has a net charge of 0.2400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: LYS 737 has a net charge of 0.0200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.320720 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): 209.8200 276.2420 ymin,ymax (A): 63.29000 140.1330 zmin,zma (A): -66.93100 13.93400 x,y,z range (A): 66.42201 76.84299 80.86500 scale (grids/A): 1.320720 object centre (A): 243.0310 101.7115 -26.49850 number of atom coordinates read : 7419 total number of charged atoms : 7172 net assigned charge : -1.707927 assigned positive charge : 1107.517 centred at (gu) : 93.07648 89.52806 87.51892 assigned negative charge : -1109.235 centred at (gu) : 93.18441 89.52258 87.25925 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 97878 reading accessible surface arcs data from file ARCDAT no. of arc points read = 64565 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 25338 mr = 64152 m= 1438 mr = 15367 m= 20 mr = 381 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 44774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1037 ## 39 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 50511 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) : 0.4402399 object centre at (A) : 243.0310 101.7115 -26.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6384750E-03 6.7391209E-03 midg,1,midg; midg,igrid,midg 1.5946192E-03 -7.3697307E-04 1,midg,midg; igrid,midg,midg -1.1860754E-03 -2.7853718E-03 gauss-seidel spectral radius is 0.9976007 estimated iterations to convergence 163 setup time was (sec) 0.7700000 now iterating at: 13:33:12 rms-change max change #iterations 3.406757 150.4032 at 10iterations 1.244582 43.43149 at 20iterations 0.4560440 15.57514 at 30iterations 0.1671409 5.528251 at 40iterations 6.1488051E-02 1.855080 at 50iterations 2.2717619E-02 0.7150688 at 60iterations 8.4938779E-03 0.3036346 at 70iterations 3.2735066E-03 0.1124668 at 80iterations 1.3971067E-03 4.3064594E-02 at 90iterations 7.1268406E-04 2.3605347E-02 at 100iterations 4.2909416E-04 1.2603998E-02 at 110iterations 2.8496515E-04 7.8291893E-03 at 120iterations finished qdiffx linear iterations at : 13:33:27 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 2.8496515E-04 7.8291893E-03 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 13:33:27 8.445u 0.249s 0:16.90 51.3% 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 Thu Jan 19 2012 at 13:33:28 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7419 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: SER 252 has a net charge of 0.2400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: LYS 737 has a net charge of 0.0200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.981080 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): 209.8200 276.2420 ymin,ymax (A): 63.29000 140.1330 zmin,zma (A): -66.93100 13.93400 x,y,z range (A): 66.42201 76.84299 80.86500 scale (grids/A): 1.981080 object centre (A): 243.0310 101.7115 -26.49850 number of atom coordinates read : 7419 total number of charged atoms : 7172 net assigned charge : -1.707927 assigned positive charge : 1107.517 centred at (gu) : 94.61432 89.29183 86.27773 assigned negative charge : -1109.235 centred at (gu) : 94.77666 89.28397 85.88879 start vw surface at 0.1900000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 229024 reading accessible surface arcs data from file ARCDAT no. of arc points read = 64565 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 95285 mr = 160270 m= 19223 mr = 70660 m= 1569 mr = 12291 m= 35 mr = 657 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 101258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 56762 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) : 1.320720 object centre at (A) : 243.0310 101.7115 -26.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6199551 0.1130626 midg,1,midg; midg,igrid,midg 5.6739826E-02 -2.8779911E-02 1,midg,midg; igrid,midg,midg -5.1812775E-02 -2.5392646E-02 gauss-seidel spectral radius is 0.9990568 estimated iterations to convergence 257 setup time was (sec) 1.490000 now iterating at: 13:33:30 rms-change max change #iterations 10.33104 267.6880 at 10iterations 5.774483 151.5621 at 20iterations 3.190863 76.59636 at 30iterations 1.755784 42.11714 at 40iterations 0.9567750 24.97136 at 50iterations 0.5212067 11.23715 at 60iterations 0.2824489 5.983519 at 70iterations 0.1529021 3.367691 at 80iterations 8.2559064E-02 1.702331 at 90iterations 4.4441696E-02 0.8790689 at 100iterations 2.3955015E-02 0.5002232 at 110iterations 1.2877807E-02 0.2415867 at 120iterations 6.9260625E-03 0.1465626 at 130iterations 3.7362068E-03 7.2040558E-02 at 140iterations 2.0114451E-03 3.6710739E-02 at 150iterations 1.0903249E-03 2.0574570E-02 at 160iterations 5.9665873E-04 1.1158466E-02 at 170iterations 3.3254435E-04 6.4907074E-03 at 180iterations finished qdiffx linear iterations at : 13:33:54 total time elapsed so far: 13.82000 # loops : 180 mean,max change (kT/e) : 3.3254435E-04 6.4907074E-03 energy calculations done at 13.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.97000 DelPhi exited at 13:33:54 13.969u 0.265s 0:26.54 53.5% 0+0k 0+0io 0pf+0w