Mon Oct 10 14:02:55 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 Mon Oct 10 2011 at 14:02:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2471 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: 0.6658437 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): -78.76400 -27.54500 ymin,ymax (A): 6.660000 60.12600 zmin,zma (A): 59.29800 110.1980 x,y,z range (A): 51.21900 53.46600 50.90000 scale (grids/A): 0.6658437 object centre (A): -53.15450 33.39300 84.74800 number of atom coordinates read : 2471 total number of charged atoms : 2332 net assigned charge : 4.000001 assigned positive charge : 369.4810 centred at (gu) : 87.66799 89.67089 92.13277 assigned negative charge : -365.4815 centred at (gu) : 87.63898 89.65478 91.98223 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7532 nv = 96 ne = 84 npr = 49342 no. pairs analyzed = 49342 no. exposed pairs = 3198 no. arc points = 22657 no. surface atoms = 1068 nbur = 1403 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 477 mr = 4055 m= 6 mr = 68 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 0.1800000 number of dielectric boundary points 3892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2028 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8543 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3608376E-08 6.7124233E-08 midg,1,midg; midg,igrid,midg 8.2536182E-09 1.3701321E-08 1,midg,midg; igrid,midg,midg 7.6455384E-09 1.0908455E-08 gauss-seidel spectral radius is 0.9883021 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 14:02:56 rms-change max change #iterations 0.1671808 23.46383 at 10iterations 1.8407606E-02 2.696167 at 20iterations 2.0614148E-03 0.3334236 at 30iterations 3.3909592E-04 4.6886444E-02 at 40iterations 1.0114325E-04 1.2349367E-02 at 50iterations finished qdiffx linear iterations at : 14:02:59 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.0114325E-04 1.2349367E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:02:59 3.452u 0.218s 0:04.04 90.5% 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 Mon Oct 10 2011 at 14:02:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2471 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: 1.997531 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): -78.76400 -27.54500 ymin,ymax (A): 6.660000 60.12600 zmin,zma (A): 59.29800 110.1980 x,y,z range (A): 51.21900 53.46600 50.90000 scale (grids/A): 1.997531 object centre (A): -53.15450 33.39300 84.74800 number of atom coordinates read : 2471 total number of charged atoms : 2332 net assigned charge : 4.000001 assigned positive charge : 369.4810 centred at (gu) : 83.00350 89.01218 96.39786 assigned negative charge : -365.4815 centred at (gu) : 82.91679 88.96430 95.94630 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80108 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22657 grid for indexing accessible points = 1.400000 m= 30962 mr = 55024 m= 5612 mr = 22496 m= 419 mr = 3423 m= 9 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 272 time to turn everything in is 0.4100000 number of dielectric boundary points 36001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 18451 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) : 0.6658437 object centre at (A) : -53.15450 33.39300 84.74800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7320292E-02 3.9963000E-02 midg,1,midg; midg,igrid,midg -3.5121843E-02 1.0221967E-02 1,midg,midg; igrid,midg,midg -1.9969870E-03 2.6295368E-02 gauss-seidel spectral radius is 0.9987444 estimated iterations to convergence 224 setup time was (sec) 0.6700000 now iterating at: 14:03:00 rms-change max change #iterations 4.561637 195.3062 at 10iterations 2.206023 73.06482 at 20iterations 1.061766 36.91116 at 30iterations 0.5157453 16.10334 at 40iterations 0.2488200 8.571567 at 50iterations 0.1204799 3.502419 at 60iterations 5.8399521E-02 1.817915 at 70iterations 2.8265290E-02 0.9278984 at 80iterations 1.3656041E-02 0.4574661 at 90iterations 6.6715167E-03 0.2132390 at 100iterations 3.2409707E-03 0.1052570 at 110iterations 1.5932516E-03 4.6917915E-02 at 120iterations finished qdiffx linear iterations at : 14:03:08 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 1.5932516E-03 4.6917915E-02 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.410000 DelPhi exited at 14:03:09 8.412u 0.250s 0:09.29 93.2% 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 Mon Oct 10 2011 at 14:03:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2471 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: 2.996297 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): -78.76400 -27.54500 ymin,ymax (A): 6.660000 60.12600 zmin,zma (A): 59.29800 110.1980 x,y,z range (A): 51.21900 53.46600 50.90000 scale (grids/A): 2.996297 object centre (A): -53.15450 33.39300 84.74800 number of atom coordinates read : 2471 total number of charged atoms : 2332 net assigned charge : 4.000001 assigned positive charge : 369.4810 centred at (gu) : 79.50512 88.51820 99.59655 assigned negative charge : -365.4815 centred at (gu) : 79.37514 88.44637 98.91940 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184918 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22657 grid for indexing accessible points = 1.400000 m= 96966 mr = 133331 m= 38628 mr = 78746 m= 10283 mr = 30585 m= 1666 mr = 7513 m= 151 mr = 1086 m= 1 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 935 time to turn everything in is 1.050000 number of dielectric boundary points 81268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 18656 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) : 1.997531 object centre at (A) : -53.15450 33.39300 84.74800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2607651 0.2569670 midg,1,midg; midg,igrid,midg -0.9901983 0.1408542 1,midg,midg; igrid,midg,midg -0.1336092 0.2061677 gauss-seidel spectral radius is 0.9992977 estimated iterations to convergence 298 setup time was (sec) 1.300000 now iterating at: 14:03:10 rms-change max change #iterations 10.51842 390.3253 at 10iterations 6.322469 142.9869 at 20iterations 3.769103 83.80042 at 30iterations 2.240081 45.84356 at 40iterations 1.327025 29.17504 at 50iterations 0.7833537 15.61454 at 60iterations 0.4614747 8.468267 at 70iterations 0.2714359 5.579944 at 80iterations 0.1594849 2.878738 at 90iterations 9.3668319E-02 1.770691 at 100iterations 5.4811269E-02 1.000512 at 110iterations 3.2165684E-02 0.5646191 at 120iterations 1.8798290E-02 0.3233256 at 130iterations 1.1010028E-02 0.1952007 at 140iterations 6.4540482E-03 0.1174011 at 150iterations 3.8009565E-03 6.4706445E-02 at 160iterations 2.2468760E-03 4.2303085E-02 at 170iterations 1.3433630E-03 2.4873734E-02 at 180iterations finished qdiffx linear iterations at : 14:03:23 total time elapsed so far: 13.91000 # loops : 180 mean,max change (kT/e) : 1.3433630E-03 2.4873734E-02 energy calculations done at 13.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.04000 DelPhi exited at 14:03:24 14.042u 0.218s 0:15.32 93.0% 0+0k 0+0io 0pf+0w