Thu Nov 3 17:12:52 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 Thu Nov 3 2011 at 17:12:52 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1082 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2643 !!! WARNING: PTR 161 has a net charge of -2.0000 !!! WARNING: PTR 162 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5940464 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): 82.28600 142.2140 ymin,ymax (A): 43.70600 95.35500 zmin,zma (A): -26.41200 27.75200 x,y,z range (A): 59.92799 51.64900 54.16400 scale (grids/A): 0.5940464 object centre (A): 112.2500 69.53049 0.6699991 number of atom coordinates read : 2643 total number of charged atoms : 2497 net assigned charge : -8.999971 assigned positive charge : 392.3036 centred at (gu) : 89.07633 90.12632 90.53452 assigned negative charge : -401.3043 centred at (gu) : 89.16708 90.03765 90.57414 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6232 nv = 96 ne = 84 npr = 53602 no. pairs analyzed = 53602 no. exposed pairs = 3472 no. arc points = 24465 no. surface atoms = 1166 nbur = 1477 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 284 mr = 3199 m= 2 mr = 20 m= 0 mr = 0 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 3299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2495 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7449298E-09 -5.0059805E-09 midg,1,midg; midg,igrid,midg -5.8259211E-09 -4.5214793E-10 1,midg,midg; igrid,midg,midg -4.2937034E-10 -4.9195963E-09 gauss-seidel spectral radius is 0.9853438 estimated iterations to convergence 68 setup time was (sec) 0.4100000 now iterating at: 17:12:52 rms-change max change #iterations 0.1015217 17.56232 at 10iterations 8.6963475E-03 1.410416 at 20iterations 9.9257939E-04 0.1762314 at 30iterations 2.3758484E-04 4.4408798E-02 at 40iterations 7.4273019E-05 1.4047623E-02 at 50iterations finished qdiffx linear iterations at : 17:12:55 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 7.4273019E-05 1.4047623E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 17:12:56 3.513u 0.311s 0:04.29 89.0% 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 Thu Nov 3 2011 at 17:12:56 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1082 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2643 !!! WARNING: PTR 161 has a net charge of -2.0000 !!! WARNING: PTR 162 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.782139 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): 82.28600 142.2140 ymin,ymax (A): 43.70600 95.35500 zmin,zma (A): -26.41200 27.75200 x,y,z range (A): 59.92799 51.64900 54.16400 scale (grids/A): 1.782139 object centre (A): 112.2500 69.53049 0.6699991 number of atom coordinates read : 2643 total number of charged atoms : 2497 net assigned charge : -8.999971 assigned positive charge : 392.3036 centred at (gu) : 87.22806 90.37817 91.60308 assigned negative charge : -401.3043 centred at (gu) : 87.50096 90.11268 91.72227 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24465 grid for indexing accessible points = 1.400000 m= 22330 mr = 46810 m= 2841 mr = 15210 m= 153 mr = 1437 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 218 time to turn everything in is 0.3400000 number of dielectric boundary points 30500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19438 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) : 0.5940464 object centre at (A) : 112.2500 69.53049 0.6699991 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9316733E-02 -1.3484566E-02 midg,1,midg; midg,igrid,midg -1.2911497E-02 -4.7887865E-04 1,midg,midg; igrid,midg,midg -1.2102227E-02 -1.3620668E-02 gauss-seidel spectral radius is 0.9984524 estimated iterations to convergence 202 setup time was (sec) 0.5600000 now iterating at: 17:12:57 rms-change max change #iterations 3.797652 237.7863 at 10iterations 1.686912 65.03014 at 20iterations 0.7522801 27.50394 at 30iterations 0.3353026 12.69520 at 40iterations 0.1495592 5.232533 at 50iterations 6.6645429E-02 2.273592 at 60iterations 2.9665027E-02 1.050039 at 70iterations 1.3253880E-02 0.4937671 at 80iterations 5.9617646E-03 0.2080815 at 90iterations 2.6977279E-03 9.7401261E-02 at 100iterations 1.2435750E-03 4.4361115E-02 at 110iterations 5.9404608E-04 2.2100449E-02 at 120iterations finished qdiffx linear iterations at : 17:13:04 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 5.9404608E-04 2.2100449E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 17:13:05 8.036u 0.236s 0:08.68 95.1% 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 Nov 3 2011 at 17:13:05 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1082 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2643 !!! WARNING: PTR 161 has a net charge of -2.0000 !!! WARNING: PTR 162 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.673208 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): 82.28600 142.2140 ymin,ymax (A): 43.70600 95.35500 zmin,zma (A): -26.41200 27.75200 x,y,z range (A): 59.92799 51.64900 54.16400 scale (grids/A): 2.673208 object centre (A): 112.2500 69.53049 0.6699991 number of atom coordinates read : 2643 total number of charged atoms : 2497 net assigned charge : -8.999971 assigned positive charge : 392.3036 centred at (gu) : 85.84200 90.56706 92.40438 assigned negative charge : -401.3043 centred at (gu) : 86.25140 90.16897 92.58334 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 159371 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24465 grid for indexing accessible points = 1.400000 m= 75535 mr = 114395 m= 23140 mr = 59882 m= 4711 mr = 17089 m= 558 mr = 3042 m= 18 mr = 295 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 677 time to turn everything in is 0.9000000 number of dielectric boundary points 68630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 19969 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) : 1.782139 object centre at (A) : 112.2500 69.53049 0.6699991 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4267780 -0.1298323 midg,1,midg; midg,igrid,midg -9.5723510E-02 4.3178596E-02 1,midg,midg; igrid,midg,midg -0.2581618 -7.1714878E-02 gauss-seidel spectral radius is 0.9992145 estimated iterations to convergence 282 setup time was (sec) 1.140000 now iterating at: 17:13:06 rms-change max change #iterations 9.285234 398.7231 at 10iterations 5.400679 159.3076 at 20iterations 3.109460 105.7751 at 30iterations 1.778641 41.92761 at 40iterations 1.019823 23.56919 at 50iterations 0.5814385 12.72848 at 60iterations 0.3302522 6.990479 at 70iterations 0.1879206 3.704455 at 80iterations 0.1065025 2.307220 at 90iterations 6.0391109E-02 1.310619 at 100iterations 3.4264527E-02 0.8220634 at 110iterations 1.9437889E-02 0.4268036 at 120iterations 1.1032282E-02 0.2404861 at 130iterations 6.2984452E-03 0.1358318 at 140iterations 3.6073115E-03 8.1211090E-02 at 150iterations 2.0999433E-03 4.4918060E-02 at 160iterations 1.2453713E-03 2.6507139E-02 at 170iterations 7.6839200E-04 1.9027710E-02 at 180iterations finished qdiffx linear iterations at : 17:13:18 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 7.6839200E-04 1.9027710E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 17:13:18 12.696u 0.370s 0:13.85 94.2% 0+0k 0+0io 0pf+0w