Wed Dec 21 14:22:18 PST 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 Wed Dec 21 2011 at 14:22:21 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 0.6403914 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): -6.098000 34.81600 ymin,ymax (A): -3.690000 48.56100 zmin,zma (A): -24.39100 31.20000 x,y,z range (A): 40.91400 52.25100 55.59100 scale (grids/A): 0.6403914 object centre (A): 14.35900 22.43550 3.404501 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 289.1040 centred at (gu) : 91.04767 92.47517 90.04683 assigned negative charge : -288.0642 centred at (gu) : 91.14695 92.66206 90.03844 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5464 nv = 96 ne = 84 npr = 40355 no. pairs analyzed = 40355 no. exposed pairs = 2451 no. arc points = 17362 no. surface atoms = 827 nbur = 1126 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 312 mr = 3049 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2900000 number of dielectric boundary points 2685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1663 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6430 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3514481E-09 2.8474976E-09 midg,1,midg; midg,igrid,midg 1.0587692E-08 -2.5087887E-08 1,midg,midg; igrid,midg,midg 8.4674863E-09 -8.3407201E-09 gauss-seidel spectral radius is 0.9873103 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 14:22:23 rms-change max change #iterations 0.1277391 19.92883 at 10iterations 1.2455946E-02 1.839867 at 20iterations 1.2549442E-03 0.1840706 at 30iterations 1.2482650E-04 2.1272659E-02 at 40iterations 1.2381063E-05 1.6937256E-03 at 50iterations finished qdiffx linear iterations at : 14:22:27 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 1.2381063E-05 1.6937256E-03 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 14:22:34 4.375u 0.451s 0:13.11 36.7% 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 Wed Dec 21 2011 at 14:22:36 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 1.921174 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): -6.098000 34.81600 ymin,ymax (A): -3.690000 48.56100 zmin,zma (A): -24.39100 31.20000 x,y,z range (A): 40.91400 52.25100 55.59100 scale (grids/A): 1.921174 object centre (A): 14.35900 22.43550 3.404501 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 289.1040 centred at (gu) : 93.14317 97.42554 90.14047 assigned negative charge : -288.0642 centred at (gu) : 93.44106 97.98611 90.11552 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 59130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17362 grid for indexing accessible points = 1.400000 m= 22090 mr = 40818 m= 3479 mr = 16972 m= 172 mr = 2332 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2155 time to turn everything in is 0.5800000 number of dielectric boundary points 24697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 14345 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) : 0.6403914 object centre at (A) : 14.35900 22.43550 3.404501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1938178E-02 7.6321005E-03 midg,1,midg; midg,igrid,midg 3.6892928E-02 -1.7708302E-02 1,midg,midg; igrid,midg,midg 7.9838997E-03 -6.6297483E-03 gauss-seidel spectral radius is 0.9985788 estimated iterations to convergence 210 setup time was (sec) 0.9400000 now iterating at: 14:22:37 rms-change max change #iterations 3.674767 166.6561 at 10iterations 1.690662 65.38203 at 20iterations 0.7857509 26.98606 at 30iterations 0.3595988 12.84442 at 40iterations 0.1664365 5.265570 at 50iterations 7.6454498E-02 2.772506 at 60iterations 3.5195429E-02 1.273750 at 70iterations 1.6236998E-02 0.5424419 at 80iterations 7.4997707E-03 0.2667389 at 90iterations 3.4613726E-03 0.1257401 at 100iterations 1.5938119E-03 5.4400444E-02 at 110iterations 7.3533657E-04 2.5756359E-02 at 120iterations finished qdiffx linear iterations at : 14:22:48 total time elapsed so far: 11.32000 # loops : 120 mean,max change (kT/e) : 7.3533657E-04 2.5756359E-02 energy calculations done at 11.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.51000 DelPhi exited at 14:22:56 11.508u 0.486s 0:21.33 56.1% 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 Wed Dec 21 2011 at 14:22:58 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 2.881762 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): -6.098000 34.81600 ymin,ymax (A): -3.690000 48.56100 zmin,zma (A): -24.39100 31.20000 x,y,z range (A): 40.91400 52.25100 55.59100 scale (grids/A): 2.881762 object centre (A): 14.35900 22.43550 3.404501 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 289.1040 centred at (gu) : 94.71487 101.1384 90.21067 assigned negative charge : -288.0642 centred at (gu) : 95.16160 101.9792 90.17332 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 136394 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17362 grid for indexing accessible points = 1.400000 m= 70677 mr = 98732 m= 26797 mr = 58664 m= 6346 mr = 22461 m= 740 mr = 4946 m= 41 mr = 503 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 7202 time to turn everything in is 1.460000 number of dielectric boundary points 55684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 14568 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) : 1.921174 object centre at (A) : 14.35900 22.43550 3.404501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.009196 -2.0049768E-02 midg,1,midg; midg,igrid,midg 0.3668274 -0.1737612 1,midg,midg; igrid,midg,midg 5.2342497E-02 -4.0889993E-02 gauss-seidel spectral radius is 0.9992315 estimated iterations to convergence 285 setup time was (sec) 1.880000 now iterating at: 14:23:01 rms-change max change #iterations 8.635673 372.6946 at 10iterations 4.958454 124.8771 at 20iterations 2.816738 61.07541 at 30iterations 1.601286 34.70850 at 40iterations 0.9097530 19.90527 at 50iterations 0.5165182 10.27175 at 60iterations 0.2925501 6.238214 at 70iterations 0.1659020 3.302869 at 80iterations 9.4283998E-02 2.028191 at 90iterations 5.3319812E-02 1.116119 at 100iterations 3.0259455E-02 0.6360931 at 110iterations 1.7145328E-02 0.3378181 at 120iterations 9.7289197E-03 0.1971741 at 130iterations 5.5106510E-03 0.1135807 at 140iterations 3.1195884E-03 7.5156271E-02 at 150iterations 1.7733832E-03 3.4118652E-02 at 160iterations 1.0038253E-03 1.9977570E-02 at 170iterations 5.7073677E-04 1.1886597E-02 at 180iterations finished qdiffx linear iterations at : 14:23:19 total time elapsed so far: 19.11000 # loops : 180 mean,max change (kT/e) : 5.7073677E-04 1.1886597E-02 energy calculations done at 19.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.30000 DelPhi exited at 14:23:20 19.299u 0.528s 0:21.57 91.8% 0+0k 0+0io 0pf+0w