Mon Oct 10 14:12:32 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 14:12:32 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 !!! WARNING: HIR 121 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6425645 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): 5.286000 60.68900 ymin,ymax (A): 2.911000 49.20800 zmin,zma (A): 13.85600 55.05200 x,y,z range (A): 55.40300 46.29700 41.19600 scale (grids/A): 0.6425645 object centre (A): 32.98750 26.05950 34.45400 number of atom coordinates read : 1956 total number of charged atoms : 1823 net assigned charge : 4.014007 assigned positive charge : 292.6598 centred at (gu) : 87.78314 89.95909 89.59576 assigned negative charge : -288.6459 centred at (gu) : 87.86989 90.01042 89.60992 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5337 nv = 96 ne = 84 npr = 40167 no. pairs analyzed = 40167 no. exposed pairs = 2458 no. arc points = 17132 no. surface atoms = 832 nbur = 1124 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 284 mr = 2806 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1646 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6332 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0051530E-09 4.3697255E-09 midg,1,midg; midg,igrid,midg 1.0869355E-08 1.2668698E-09 1,midg,midg; igrid,midg,midg 2.2562720E-08 -1.1732030E-09 gauss-seidel spectral radius is 0.9873924 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 14:12:32 rms-change max change #iterations 0.1295000 20.34202 at 10iterations 1.3105009E-02 2.512730 at 20iterations 1.3152120E-03 0.2168198 at 30iterations 1.4144603E-04 2.1575928E-02 at 40iterations 1.9227600E-05 3.0670166E-03 at 50iterations finished qdiffx linear iterations at : 14:12:35 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 1.9227600E-05 3.0670166E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 14:12:36 3.300u 0.175s 0:03.84 90.3% 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 14:12:36 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 !!! WARNING: HIR 121 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: 1.927693 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): 5.286000 60.68900 ymin,ymax (A): 2.911000 49.20800 zmin,zma (A): 13.85600 55.05200 x,y,z range (A): 55.40300 46.29700 41.19600 scale (grids/A): 1.927693 object centre (A): 32.98750 26.05950 34.45400 number of atom coordinates read : 1956 total number of charged atoms : 1823 net assigned charge : 4.014007 assigned positive charge : 292.6598 centred at (gu) : 83.34928 89.87692 88.78708 assigned negative charge : -288.6459 centred at (gu) : 83.60970 90.03106 88.82973 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 57122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17132 grid for indexing accessible points = 1.400000 m= 20099 mr = 38684 m= 3239 mr = 14387 m= 196 mr = 1896 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 284 time to turn everything in is 0.4700000 number of dielectric boundary points 25645 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14358 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) : 0.6425645 object centre at (A) : 32.98750 26.05950 34.45400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9400008E-02 5.7873717E-03 midg,1,midg; midg,igrid,midg 2.2169435E-02 4.5303372E-03 1,midg,midg; igrid,midg,midg -2.3722162E-02 -2.6766056E-02 gauss-seidel spectral radius is 0.9985973 estimated iterations to convergence 212 setup time was (sec) 0.7500000 now iterating at: 14:12:37 rms-change max change #iterations 3.692399 181.9012 at 10iterations 1.702161 66.02484 at 20iterations 0.7920513 27.29822 at 30iterations 0.3667176 12.87252 at 40iterations 0.1704048 6.286662 at 50iterations 7.8818321E-02 2.839166 at 60iterations 3.6447451E-02 1.212349 at 70iterations 1.6872093E-02 0.6094894 at 80iterations 7.9094209E-03 0.2779751 at 90iterations 3.6958582E-03 0.1280327 at 100iterations 1.7255248E-03 6.0434341E-02 at 110iterations 8.1357453E-04 2.9632568E-02 at 120iterations finished qdiffx linear iterations at : 14:12:43 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 8.1357453E-04 2.9632568E-02 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 14:12:44 7.292u 0.217s 0:08.04 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 14:12:44 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 !!! WARNING: HIR 121 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: 2.891540 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): 5.286000 60.68900 ymin,ymax (A): 2.911000 49.20800 zmin,zma (A): 13.85600 55.05200 x,y,z range (A): 55.40300 46.29700 41.19600 scale (grids/A): 2.891540 object centre (A): 32.98750 26.05950 34.45400 number of atom coordinates read : 1956 total number of charged atoms : 1823 net assigned charge : 4.014007 assigned positive charge : 292.6598 centred at (gu) : 80.02399 89.81534 88.18059 assigned negative charge : -288.6459 centred at (gu) : 80.41448 90.04652 88.24448 start vw surface at 0.1900000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 131856 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17132 grid for indexing accessible points = 1.400000 m= 65380 mr = 93948 m= 23140 mr = 52423 m= 5645 mr = 18292 m= 836 mr = 4026 m= 41 mr = 452 m= 0 mr = 9 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 995 time to turn everything in is 1.100000 number of dielectric boundary points 57748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 14584 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) : 1.927693 object centre at (A) : 32.98750 26.05950 34.45400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2057970 3.1029923E-02 midg,1,midg; midg,igrid,midg 0.1908781 -7.6475730E-03 1,midg,midg; igrid,midg,midg -0.4774762 -0.4236597 gauss-seidel spectral radius is 0.9992347 estimated iterations to convergence 285 setup time was (sec) 1.390000 now iterating at: 14:12:45 rms-change max change #iterations 8.731745 474.9692 at 10iterations 5.052841 124.5586 at 20iterations 2.916706 70.51426 at 30iterations 1.677394 37.82583 at 40iterations 0.9621906 23.60319 at 50iterations 0.5500302 13.83853 at 60iterations 0.3158307 6.952947 at 70iterations 0.1801057 4.502189 at 80iterations 0.1030613 2.444862 at 90iterations 5.8605608E-02 1.368526 at 100iterations 3.3439685E-02 0.6629410 at 110iterations 1.9097880E-02 0.3911474 at 120iterations 1.0883300E-02 0.2306099 at 130iterations 6.2179402E-03 0.1238816 at 140iterations 3.5529714E-03 7.4752808E-02 at 150iterations 2.0367284E-03 4.2993546E-02 at 160iterations 1.1749199E-03 2.4618030E-02 at 170iterations 6.8118342E-04 1.5165329E-02 at 180iterations finished qdiffx linear iterations at : 14:12:55 total time elapsed so far: 11.35000 # loops : 180 mean,max change (kT/e) : 6.8118342E-04 1.5165329E-02 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.54000 DelPhi exited at 14:12:56 11.538u 0.217s 0:12.12 96.8% 0+0k 0+0io 0pf+0w