Mon Oct 10 18:48:19 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 18:48:19 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2409 !!! WARNING: HIR 257 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5964448 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): -11.39400 48.29300 ymin,ymax (A): 61.66500 115.6370 zmin,zma (A): 45.08800 87.98900 x,y,z range (A): 59.68700 53.97200 42.90100 scale (grids/A): 0.5964448 object centre (A): 18.44950 88.65100 66.53850 number of atom coordinates read : 2409 total number of charged atoms : 2270 net assigned charge : -0.9859921 assigned positive charge : 364.6668 centred at (gu) : 87.80569 90.95545 90.96020 assigned negative charge : -365.6535 centred at (gu) : 87.85347 91.00113 91.07824 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5753 nv = 96 ne = 84 npr = 48397 no. pairs analyzed = 48397 no. exposed pairs = 3032 no. arc points = 21075 no. surface atoms = 1015 nbur = 1394 mkacc time = 0.1100000 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 = 1.456000 m= 273 mr = 3123 m= 0 mr = 26 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2106 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7142 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5622859E-09 -5.0101074E-09 midg,1,midg; midg,igrid,midg 8.2644253E-10 -2.1883020E-09 1,midg,midg; igrid,midg,midg 1.8584715E-09 -1.1054085E-09 gauss-seidel spectral radius is 0.9854377 estimated iterations to convergence 68 setup time was (sec) 0.4900000 now iterating at: 18:48:20 rms-change max change #iterations 0.1036935 16.06849 at 10iterations 8.7598553E-03 1.474159 at 20iterations 7.7071827E-04 0.1162214 at 30iterations 1.0189391E-04 1.9899368E-02 at 40iterations 2.2037035E-05 4.7354698E-03 at 50iterations finished qdiffx linear iterations at : 18:48:22 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 2.2037035E-05 4.7354698E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 18:48:23 3.164u 0.157s 0:03.61 91.6% 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 18:48:23 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2409 !!! WARNING: HIR 257 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.789334 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): -11.39400 48.29300 ymin,ymax (A): 61.66500 115.6370 zmin,zma (A): 45.08800 87.98900 x,y,z range (A): 59.68700 53.97200 42.90100 scale (grids/A): 1.789334 object centre (A): 18.44950 88.65100 66.53850 number of atom coordinates read : 2409 total number of charged atoms : 2270 net assigned charge : -0.9859921 assigned positive charge : 364.6668 centred at (gu) : 83.41646 92.86590 92.87985 assigned negative charge : -365.6535 centred at (gu) : 83.56023 93.00318 93.23456 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21075 grid for indexing accessible points = 1.400000 m= 21848 mr = 43658 m= 2890 mr = 15847 m= 109 mr = 1672 m= 0 mr = 23 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1224 time to turn everything in is 0.4600000 number of dielectric boundary points 26405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 17725 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) : 0.5964448 object centre at (A) : 18.44950 88.65100 66.53850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7293731E-03 -6.9580888E-03 midg,1,midg; midg,igrid,midg 1.5936872E-02 -1.2044914E-02 1,midg,midg; igrid,midg,midg -1.2148095E-02 -1.4843521E-02 gauss-seidel spectral radius is 0.9984340 estimated iterations to convergence 200 setup time was (sec) 0.7300000 now iterating at: 18:48:23 rms-change max change #iterations 3.643697 163.1254 at 10iterations 1.601316 65.31438 at 20iterations 0.7132424 25.95167 at 30iterations 0.3155939 11.90913 at 40iterations 0.1404805 4.771290 at 50iterations 6.2273078E-02 2.203437 at 60iterations 2.7605310E-02 1.017075 at 70iterations 1.2320072E-02 0.4511108 at 80iterations 5.4719276E-03 0.2257385 at 90iterations 2.4589219E-03 8.9553833E-02 at 100iterations 1.1072657E-03 4.0428162E-02 at 110iterations 5.1047810E-04 1.7463684E-02 at 120iterations finished qdiffx linear iterations at : 18:48:30 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 5.1047810E-04 1.7463684E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 18:48:30 7.013u 0.185s 0:07.52 95.6% 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 18:48:30 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2409 !!! WARNING: HIR 257 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.684001 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): -11.39400 48.29300 ymin,ymax (A): 61.66500 115.6370 zmin,zma (A): 45.08800 87.98900 x,y,z range (A): 59.68700 53.97200 42.90100 scale (grids/A): 2.684001 object centre (A): 18.44950 88.65100 66.53850 number of atom coordinates read : 2409 total number of charged atoms : 2270 net assigned charge : -0.9859921 assigned positive charge : 364.6668 centred at (gu) : 80.12447 94.29870 94.31978 assigned negative charge : -365.6535 centred at (gu) : 80.34025 94.50467 94.85178 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 145539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21075 grid for indexing accessible points = 1.400000 m= 71688 mr = 106118 m= 24691 mr = 58204 m= 4978 mr = 19555 m= 469 mr = 3559 m= 14 mr = 255 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 4105 time to turn everything in is 1.080000 number of dielectric boundary points 59688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 18154 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) : 1.789334 object centre at (A) : 18.44950 88.65100 66.53850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1861459E-02 -6.5542124E-02 midg,1,midg; midg,igrid,midg 0.2656414 -0.1869019 1,midg,midg; igrid,midg,midg -0.1868179 -7.4929348E-04 gauss-seidel spectral radius is 0.9991969 estimated iterations to convergence 279 setup time was (sec) 1.370000 now iterating at: 18:48:32 rms-change max change #iterations 8.875862 269.0329 at 10iterations 5.117244 125.6515 at 20iterations 2.904354 68.57181 at 30iterations 1.653796 37.47813 at 40iterations 0.9364478 21.75481 at 50iterations 0.5288618 11.36612 at 60iterations 0.2982377 6.939131 at 70iterations 0.1681185 3.564037 at 80iterations 9.4499230E-02 2.032875 at 90iterations 5.3154960E-02 1.027451 at 100iterations 2.9869435E-02 0.7417870 at 110iterations 1.6760390E-02 0.3394184 at 120iterations 9.4235893E-03 0.1841011 at 130iterations 5.2854083E-03 9.9622250E-02 at 140iterations 2.9690671E-03 6.1418533E-02 at 150iterations 1.6737281E-03 3.2509327E-02 at 160iterations 9.3794195E-04 1.9615173E-02 at 170iterations 5.2889285E-04 1.1001587E-02 at 180iterations finished qdiffx linear iterations at : 18:48:42 total time elapsed so far: 11.40000 # loops : 180 mean,max change (kT/e) : 5.2889285E-04 1.1001587E-02 energy calculations done at 11.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 18:48:42 11.585u 0.167s 0:12.04 97.5% 0+0k 0+0io 0pf+0w