Tue Oct 11 06:57:35 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 06:57:35 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: HIR 199 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: 0.5489421 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): -20.17400 44.67800 ymin,ymax (A): 19.67600 76.04700 zmin,zma (A): -70.34900 -21.03300 x,y,z range (A): 64.85201 56.37100 49.31600 scale (grids/A): 0.5489421 object centre (A): 12.25200 47.86150 -45.69100 number of atom coordinates read : 3043 total number of charged atoms : 2903 net assigned charge : -0.4859801 assigned positive charge : 450.1855 centred at (gu) : 89.86749 90.01526 90.22108 assigned negative charge : -450.6720 centred at (gu) : 89.84617 90.21257 90.24229 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5899 nv = 96 ne = 84 npr = 63043 no. pairs analyzed = 63043 no. exposed pairs = 3905 no. arc points = 27593 no. surface atoms = 1317 nbur = 1726 mkacc time = 0.1700000 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= 244 mr = 2987 m= 0 mr = 11 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2846 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7762 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2077603E-10 -2.0232491E-10 midg,1,midg; midg,igrid,midg 1.4124435E-09 -1.5601996E-09 1,midg,midg; igrid,midg,midg -1.9886162E-10 1.2440390E-10 gauss-seidel spectral radius is 0.9828960 estimated iterations to convergence 63 setup time was (sec) 0.6500000 now iterating at: 06:57:36 rms-change max change #iterations 7.8147799E-02 14.22380 at 10iterations 5.1915064E-03 0.9525108 at 20iterations 3.5735351E-04 5.8494568E-02 at 30iterations 2.3895924E-05 4.3182373E-03 at 40iterations 1.6571230E-06 2.9182434E-04 at 50iterations finished qdiffx linear iterations at : 06:57:39 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 1.6571230E-06 2.9182434E-04 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 06:57:40 4.100u 0.276s 0:04.67 93.5% 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 Tue Oct 11 2011 at 06:57:40 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 = 3043 !!! WARNING: HIR 199 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: 1.646827 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): -20.17400 44.67800 ymin,ymax (A): 19.67600 76.04700 zmin,zma (A): -70.34900 -21.03300 x,y,z range (A): 64.85201 56.37100 49.31600 scale (grids/A): 1.646827 object centre (A): 12.25200 47.86150 -45.69100 number of atom coordinates read : 3043 total number of charged atoms : 2903 net assigned charge : -0.4859801 assigned positive charge : 450.1855 centred at (gu) : 89.60207 90.04525 90.66282 assigned negative charge : -450.6720 centred at (gu) : 89.53814 90.63731 90.72655 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 64202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27593 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20590 mr = 42598 m= 2302 mr = 14253 m= 54 mr = 1173 m= 0 mr = 5 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 717 time to turn everything in is 0.5800000 number of dielectric boundary points 29119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 291 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 22309 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) : 0.5489421 object centre at (A) : 12.25200 47.86150 -45.69100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1351587E-03 1.3348269E-02 midg,1,midg; midg,igrid,midg -1.5268204E-04 -1.1523863E-02 1,midg,midg; igrid,midg,midg 4.3384987E-03 -3.7388646E-03 gauss-seidel spectral radius is 0.9982282 estimated iterations to convergence 189 setup time was (sec) 0.8900000 now iterating at: 06:57:41 rms-change max change #iterations 3.414733 187.6837 at 10iterations 1.430852 54.91092 at 20iterations 0.6016768 20.76530 at 30iterations 0.2535236 10.05328 at 40iterations 0.1066389 3.983804 at 50iterations 4.4662796E-02 1.659880 at 60iterations 1.8915923E-02 0.7200699 at 70iterations 7.9440903E-03 0.2894363 at 80iterations 3.3529364E-03 0.1143761 at 90iterations 1.4110963E-03 5.3058624E-02 at 100iterations 5.9523270E-04 2.3162842E-02 at 110iterations 2.5091608E-04 9.0255737E-03 at 120iterations finished qdiffx linear iterations at : 06:57:49 total time elapsed so far: 9.070000 # loops : 120 mean,max change (kT/e) : 2.5091608E-04 9.0255737E-03 energy calculations done at 9.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.240000 DelPhi exited at 06:57:50 9.246u 0.304s 0:10.34 92.2% 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 06:57:50 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 = 3043 !!! WARNING: HIR 199 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: 2.470240 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): -20.17400 44.67800 ymin,ymax (A): 19.67600 76.04700 zmin,zma (A): -70.34900 -21.03300 x,y,z range (A): 64.85201 56.37100 49.31600 scale (grids/A): 2.470240 object centre (A): 12.25200 47.86150 -45.69100 number of atom coordinates read : 3043 total number of charged atoms : 2903 net assigned charge : -0.4859801 assigned positive charge : 450.1855 centred at (gu) : 89.40305 90.06785 90.99401 assigned negative charge : -450.6720 centred at (gu) : 89.30706 90.95595 91.08964 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 148935 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27593 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 69101 mr = 104191 m= 21651 mr = 54597 m= 3755 mr = 16553 m= 205 mr = 2485 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 2340 time to turn everything in is 1.450000 number of dielectric boundary points 65747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 23199 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) : 1.646827 object centre at (A) : 12.25200 47.86150 -45.69100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1630369 0.2286264 midg,1,midg; midg,igrid,midg -1.5506529E-03 -0.1417940 1,midg,midg; igrid,midg,midg 4.1763239E-02 4.1167654E-02 gauss-seidel spectral radius is 0.9991539 estimated iterations to convergence 272 setup time was (sec) 1.770000 now iterating at: 06:57:52 rms-change max change #iterations 8.823367 265.4856 at 10iterations 4.949639 119.5929 at 20iterations 2.772540 63.82364 at 30iterations 1.549112 33.37528 at 40iterations 0.8629127 16.77657 at 50iterations 0.4788050 10.09470 at 60iterations 0.2652877 5.854624 at 70iterations 0.1473898 3.308731 at 80iterations 8.1341937E-02 1.818948 at 90iterations 4.5014970E-02 0.9092045 at 100iterations 2.4867661E-02 0.5071945 at 110iterations 1.3778886E-02 0.3023586 at 120iterations 7.5954837E-03 0.1443405 at 130iterations 4.2030159E-03 8.3306670E-02 at 140iterations 2.3196482E-03 5.0193548E-02 at 150iterations 1.2791033E-03 2.4741292E-02 at 160iterations 7.0564193E-04 1.3917923E-02 at 170iterations 3.8998693E-04 7.7714920E-03 at 180iterations finished qdiffx linear iterations at : 06:58:06 total time elapsed so far: 15.14000 # loops : 180 mean,max change (kT/e) : 3.8998693E-04 7.7714920E-03 energy calculations done at 15.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.32000 DelPhi exited at 06:58:06 15.319u 0.305s 0:15.94 97.9% 0+0k 0+0io 0pf+0w