Tue Oct 11 03:24:35 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 Tue Oct 11 2011 at 03:24:35 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 = 4233 !!! WARNING: HIR 58 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5456106 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): -27.55100 30.90200 ymin,ymax (A): -25.08800 34.80600 zmin,zma (A): -30.89600 34.35200 x,y,z range (A): 58.45300 59.89400 65.24800 scale (grids/A): 0.5456106 object centre (A): 1.675501 4.858999 1.727999 number of atom coordinates read : 4233 total number of charged atoms : 4091 net assigned charge : -1.985953 assigned positive charge : 637.2656 centred at (gu) : 92.09423 90.22448 90.70613 assigned negative charge : -639.2551 centred at (gu) : 92.03445 90.31998 90.70598 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8127 nv = 96 ne = 84 npr = 85270 no. pairs analyzed = 85270 no. exposed pairs = 5527 no. arc points = 39191 no. surface atoms = 1861 nbur = 2372 mkacc time = 0.2300000 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 = 1.568000 m= 339 mr = 4080 m= 5 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3925 ## 522 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 10702 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1232008E-10 -1.5447264E-10 midg,1,midg; midg,igrid,midg 7.1101386E-10 -1.0976201E-09 1,midg,midg; igrid,midg,midg -4.1515569E-10 7.2937612E-10 gauss-seidel spectral radius is 0.9827828 estimated iterations to convergence 63 setup time was (sec) 0.8000000 now iterating at: 03:24:36 rms-change max change #iterations 9.0045691E-02 12.90036 at 10iterations 5.9773983E-03 0.9012508 at 20iterations 4.3854077E-04 6.5759659E-02 at 30iterations 5.0638115E-05 8.9221001E-03 at 40iterations 1.0922558E-05 2.1922588E-03 at 50iterations finished qdiffx linear iterations at : 03:24:41 total time elapsed so far: 5.750000 # loops : 50 mean,max change (kT/e) : 1.0922558E-05 2.1922588E-03 energy calculations done at 5.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.910000 DelPhi exited at 03:24:41 5.917u 0.431s 0:06.70 94.6% 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 Tue Oct 11 2011 at 03:24:41 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 = 4233 !!! WARNING: HIR 58 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.636832 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): -27.55100 30.90200 ymin,ymax (A): -25.08800 34.80600 zmin,zma (A): -30.89600 34.35200 x,y,z range (A): 58.45300 59.89400 65.24800 scale (grids/A): 1.636832 object centre (A): 1.675501 4.858999 1.727999 number of atom coordinates read : 4233 total number of charged atoms : 4091 net assigned charge : -1.985953 assigned positive charge : 637.2656 centred at (gu) : 96.28098 90.67210 92.11660 assigned negative charge : -639.2551 centred at (gu) : 96.10270 90.95918 92.11726 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89992 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39191 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25914 mr = 59711 m= 2531 mr = 17052 m= 63 mr = 1160 m= 0 mr = 6 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 40571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 486 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 31295 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) : 0.5456106 object centre at (A) : 1.675501 4.858999 1.727999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8082241E-02 -3.6511716E-02 midg,1,midg; midg,igrid,midg 1.4214075E-02 -1.4106875E-02 1,midg,midg; igrid,midg,midg 2.3540498E-03 1.9897247E-02 gauss-seidel spectral radius is 0.9983238 estimated iterations to convergence 194 setup time was (sec) 1.180000 now iterating at: 03:24:43 rms-change max change #iterations 4.115921 178.7989 at 10iterations 1.770761 56.26443 at 20iterations 0.7610288 26.80574 at 30iterations 0.3273486 9.901416 at 40iterations 0.1411475 4.768209 at 50iterations 6.0991526E-02 1.747818 at 60iterations 2.6196310E-02 0.8936639 at 70iterations 1.1320961E-02 0.4166393 at 80iterations 4.9025179E-03 0.1451011 at 90iterations 2.1092191E-03 6.7548752E-02 at 100iterations 9.1429590E-04 3.0847549E-02 at 110iterations 3.9704508E-04 1.2367249E-02 at 120iterations finished qdiffx linear iterations at : 03:24:56 total time elapsed so far: 13.97000 # loops : 120 mean,max change (kT/e) : 3.9704508E-04 1.2367249E-02 energy calculations done at 13.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.13000 DelPhi exited at 03:24:57 14.133u 0.503s 0:15.17 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 Tue Oct 11 2011 at 03:24:57 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 = 4233 !!! WARNING: HIR 58 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.455248 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): -27.55100 30.90200 ymin,ymax (A): -25.08800 34.80600 zmin,zma (A): -30.89600 34.35200 x,y,z range (A): 58.45300 59.89400 65.24800 scale (grids/A): 2.455248 object centre (A): 1.675501 4.858999 1.727999 number of atom coordinates read : 4233 total number of charged atoms : 4091 net assigned charge : -1.985953 assigned positive charge : 637.2656 centred at (gu) : 99.42135 91.00773 93.17458 assigned negative charge : -639.2551 centred at (gu) : 99.15395 91.43861 93.17581 start vw surface at 0.1500000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 209064 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39191 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 91520 mr = 146573 m= 24298 mr = 70755 m= 3920 mr = 17668 m= 290 mr = 2445 m= 3 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.860000 number of dielectric boundary points 91532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 32692 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) : 1.636832 object centre at (A) : 1.675501 4.858999 1.727999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3067883 -0.8462014 midg,1,midg; midg,igrid,midg 0.1718717 -0.1849221 1,midg,midg; igrid,midg,midg 3.1743906E-02 0.2751758 gauss-seidel spectral radius is 0.9992204 estimated iterations to convergence 283 setup time was (sec) 2.260000 now iterating at: 03:24:59 rms-change max change #iterations 10.71836 444.1985 at 10iterations 6.248519 142.1286 at 20iterations 3.628132 71.80482 at 30iterations 2.090461 44.20972 at 40iterations 1.199053 24.27385 at 50iterations 0.6881560 16.27090 at 60iterations 0.3918629 8.159867 at 70iterations 0.2237355 5.058496 at 80iterations 0.1271532 2.306660 at 90iterations 7.2285011E-02 1.381130 at 100iterations 4.1044649E-02 0.7485420 at 110iterations 2.3306033E-02 0.4281464 at 120iterations 1.3272228E-02 0.2292095 at 130iterations 7.5034788E-03 0.1291161 at 140iterations 4.2567020E-03 7.4600220E-02 at 150iterations 2.4121075E-03 4.1945592E-02 at 160iterations 1.3688811E-03 2.5127411E-02 at 170iterations 7.7715551E-04 1.4295578E-02 at 180iterations finished qdiffx linear iterations at : 03:25:21 total time elapsed so far: 23.77000 # loops : 180 mean,max change (kT/e) : 7.7715551E-04 1.4295578E-02 energy calculations done at 23.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.93000 DelPhi exited at 03:25:22 23.934u 0.543s 0:24.95 98.0% 0+0k 0+0io 0pf+0w