Mon Oct 10 13:56:45 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 13:56:45 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5006 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: SEP 674 has a net charge of -0.4750 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5595373 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): 3.191000 64.75000 ymin,ymax (A): -8.671000 52.58900 zmin,zma (A): -1.898000 61.72600 x,y,z range (A): 61.55900 61.26000 63.62400 scale (grids/A): 0.5595373 object centre (A): 33.97050 21.95900 29.91400 number of atom coordinates read : 5006 total number of charged atoms : 4888 net assigned charge : 1.160050 assigned positive charge : 778.1867 centred at (gu) : 88.39592 89.38524 89.11842 assigned negative charge : -777.0325 centred at (gu) : 88.23132 89.40388 89.11175 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 10180 nv = 96 ne = 84 npr = 100692 no. pairs analyzed = 100692 no. exposed pairs = 5977 no. arc points = 40574 no. surface atoms = 2019 nbur = 2987 mkacc time = 0.2800000 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 = 1.512000 m= 474 mr = 5716 m= 0 mr = 23 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4140 ## 447 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 13397 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2535498E-11 2.4646576E-10 midg,1,midg; midg,igrid,midg 6.1702482E-10 -1.5075166E-10 1,midg,midg; igrid,midg,midg -4.4864406E-09 2.1908488E-09 gauss-seidel spectral radius is 0.9836721 estimated iterations to convergence 64 setup time was (sec) 0.8700000 now iterating at: 13:56:48 rms-change max change #iterations 0.1147190 14.93148 at 10iterations 9.8835155E-03 1.379242 at 20iterations 2.6382611E-03 0.3530598 at 30iterations 1.2951097E-03 0.1609573 at 40iterations 6.5792672E-04 7.7480316E-02 at 50iterations finished qdiffx linear iterations at : 13:56:53 total time elapsed so far: 5.090000 # loops : 50 mean,max change (kT/e) : 6.5792672E-04 7.7480316E-02 energy calculations done at 5.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.240000 DelPhi exited at 13:56:53 5.243u 0.614s 0:07.85 74.5% 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 13:56:53 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5006 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: SEP 674 has a net charge of -0.4750 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.678612 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): 3.191000 64.75000 ymin,ymax (A): -8.671000 52.58900 zmin,zma (A): -1.898000 61.72600 x,y,z range (A): 61.55900 61.26000 63.62400 scale (grids/A): 1.678612 object centre (A): 33.97050 21.95900 29.91400 number of atom coordinates read : 5006 total number of charged atoms : 4888 net assigned charge : 1.160050 assigned positive charge : 778.1867 centred at (gu) : 85.18669 88.15439 87.35345 assigned negative charge : -777.0325 centred at (gu) : 84.69382 88.21149 87.33498 start vw surface at 0.1600000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 113047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40574 grid for indexing accessible points = 1.400000 m= 38639 mr = 81410 m= 4938 mr = 27274 m= 178 mr = 2622 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 45481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 392 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 37590 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) : 0.5595373 object centre at (A) : 33.97050 21.95900 29.91400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3394139E-02 -2.8044939E-02 midg,1,midg; midg,igrid,midg 1.7484216E-02 1.0286995E-02 1,midg,midg; igrid,midg,midg -2.5809318E-02 3.8898524E-02 gauss-seidel spectral radius is 0.9984701 estimated iterations to convergence 203 setup time was (sec) 1.290000 now iterating at: 13:56:55 rms-change max change #iterations 4.935457 188.4158 at 10iterations 2.209466 62.93452 at 20iterations 0.9930498 30.97897 at 30iterations 0.4455477 12.58139 at 40iterations 0.2008602 5.930670 at 50iterations 9.0544716E-02 2.419857 at 60iterations 4.1100521E-02 1.098730 at 70iterations 1.8936796E-02 0.5107089 at 80iterations 9.1697667E-03 0.2550039 at 90iterations 4.8970380E-03 0.1420746 at 100iterations 3.0282196E-03 8.6082458E-02 at 110iterations 2.1245999E-03 5.7121277E-02 at 120iterations finished qdiffx linear iterations at : 13:57:07 total time elapsed so far: 13.01000 # loops : 120 mean,max change (kT/e) : 2.1245999E-03 5.7121277E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 13:57:08 13.167u 0.564s 0:14.15 96.9% 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 13:57:10 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5006 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: SEP 674 has a net charge of -0.4750 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.517918 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): 3.191000 64.75000 ymin,ymax (A): -8.671000 52.58900 zmin,zma (A): -1.898000 61.72600 x,y,z range (A): 61.55900 61.26000 63.62400 scale (grids/A): 2.517918 object centre (A): 33.97050 21.95900 29.91400 number of atom coordinates read : 5006 total number of charged atoms : 4888 net assigned charge : 1.160050 assigned positive charge : 778.1867 centred at (gu) : 82.77966 87.23110 86.02972 assigned negative charge : -777.0325 centred at (gu) : 82.04062 87.31715 86.00256 start vw surface at 0.1700000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 262898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40574 grid for indexing accessible points = 1.400000 m= 130238 mr = 198279 m= 41611 mr = 104975 m= 8085 mr = 31726 m= 759 mr = 5358 m= 17 mr = 355 m= 0 mr = 0 time to grow re-entrant surface = 1.550000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.450000 number of dielectric boundary points 102915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 2.630000 number of grid points assigned charge 39078 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) : 1.678612 object centre at (A) : 33.97050 21.95900 29.91400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4111573 -0.6344920 midg,1,midg; midg,igrid,midg 7.3215954E-02 -5.6942683E-03 1,midg,midg; igrid,midg,midg -0.3940100 0.4574526 gauss-seidel spectral radius is 0.9992655 estimated iterations to convergence 291 setup time was (sec) 2.870000 now iterating at: 13:57:17 rms-change max change #iterations 12.50955 323.8090 at 10iterations 7.428008 140.9511 at 20iterations 4.382051 89.60838 at 30iterations 2.578807 50.57932 at 40iterations 1.509937 27.11160 at 50iterations 0.8808433 18.00554 at 60iterations 0.5129479 9.339970 at 70iterations 0.2976132 4.791368 at 80iterations 0.1727408 3.110809 at 90iterations 0.1001007 1.586750 at 100iterations 5.7972934E-02 0.9728470 at 110iterations 3.3670526E-02 0.5517123 at 120iterations 1.9600792E-02 0.3389106 at 130iterations 1.1449150E-02 0.1845999 at 140iterations 6.8163979E-03 0.1136255 at 150iterations 4.1709593E-03 7.5256348E-02 at 160iterations 2.6863588E-03 5.0498962E-02 at 170iterations 1.8559474E-03 3.5423279E-02 at 180iterations finished qdiffx linear iterations at : 13:57:40 total time elapsed so far: 24.02000 # loops : 180 mean,max change (kT/e) : 1.8559474E-03 3.5423279E-02 energy calculations done at 24.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.20000 DelPhi exited at 13:57:41 24.202u 0.806s 0:30.62 81.6% 0+0k 0+0io 0pf+0w