Mon Oct 10 01:03:04 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 01:03:04 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6418462 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): -5.300000 34.94800 ymin,ymax (A): -3.324000 47.79400 zmin,zma (A): -24.44000 31.02500 x,y,z range (A): 40.24800 51.11800 55.46500 scale (grids/A): 0.6418462 object centre (A): 14.82400 22.23500 3.292500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.61091 92.76237 90.22858 assigned negative charge : -284.8263 centred at (gu) : 90.72872 92.91576 90.17527 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5504 nv = 96 ne = 84 npr = 39959 no. pairs analyzed = 39959 no. exposed pairs = 2414 no. arc points = 16979 no. surface atoms = 817 nbur = 1147 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 285 mr = 3149 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.1700000 number of dielectric boundary points 2596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1720 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6526 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8888777E-10 1.0277371E-08 midg,1,midg; midg,igrid,midg 1.0331535E-08 -1.6570970E-08 1,midg,midg; igrid,midg,midg 1.3545768E-08 -6.3962893E-09 gauss-seidel spectral radius is 0.9873659 estimated iterations to convergence 73 setup time was (sec) 0.3500000 now iterating at: 01:03:05 rms-change max change #iterations 0.1195538 18.90290 at 10iterations 1.2251622E-02 1.759914 at 20iterations 1.1909438E-03 0.1940222 at 30iterations 1.1913042E-04 1.9868851E-02 at 40iterations 1.1892201E-05 1.7986298E-03 at 50iterations finished qdiffx linear iterations at : 01:03:08 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.1892201E-05 1.7986298E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 01:03:08 3.393u 0.180s 0:03.88 92.0% 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 01:03:08 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 = 1964 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: 1.925539 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): -5.300000 34.94800 ymin,ymax (A): -3.324000 47.79400 zmin,zma (A): -24.44000 31.02500 x,y,z range (A): 40.24800 51.11800 55.46500 scale (grids/A): 1.925539 object centre (A): 14.82400 22.23500 3.292500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.83279 98.28720 90.68572 assigned negative charge : -284.8263 centred at (gu) : 92.18642 98.74728 90.52584 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 22350 mr = 41320 m= 3495 mr = 17377 m= 196 mr = 2363 m= 4 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2215 time to turn everything in is 0.3100000 number of dielectric boundary points 24210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 14472 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) : 0.6418462 object centre at (A) : 14.82400 22.23500 3.292500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4933561E-02 1.4074589E-02 midg,1,midg; midg,igrid,midg 3.2533009E-02 -9.4327312E-03 1,midg,midg; igrid,midg,midg 1.0474772E-02 -5.0808531E-03 gauss-seidel spectral radius is 0.9985833 estimated iterations to convergence 211 setup time was (sec) 0.5300000 now iterating at: 01:03:09 rms-change max change #iterations 3.642039 180.8238 at 10iterations 1.682816 66.01112 at 20iterations 0.7804378 29.06456 at 30iterations 0.3606724 13.22241 at 40iterations 0.1660146 5.748677 at 50iterations 7.6597229E-02 2.915554 at 60iterations 3.5350982E-02 1.297728 at 70iterations 1.6323272E-02 0.5368567 at 80iterations 7.5390479E-03 0.2561750 at 90iterations 3.4804225E-03 0.1173210 at 100iterations 1.6130042E-03 5.2714348E-02 at 110iterations 7.4436539E-04 2.6249647E-02 at 120iterations finished qdiffx linear iterations at : 01:03:16 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 7.4436539E-04 2.6249647E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 01:03:16 7.720u 0.199s 0:08.26 95.7% 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 Mon Oct 10 2011 at 01:03:17 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 = 1964 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: 2.888308 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): -5.300000 34.94800 ymin,ymax (A): -3.324000 47.79400 zmin,zma (A): -24.44000 31.02500 x,y,z range (A): 40.24800 51.11800 55.46500 scale (grids/A): 2.888308 object centre (A): 14.82400 22.23500 3.292500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.74928 102.4308 91.02858 assigned negative charge : -284.8263 centred at (gu) : 93.27967 103.1211 90.78879 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 137192 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 71623 mr = 99913 m= 26850 mr = 59979 m= 6151 mr = 22619 m= 855 mr = 4861 m= 58 mr = 641 m= 0 mr = 32 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 7824 time to turn everything in is 0.7800000 number of dielectric boundary points 54684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 14656 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) : 1.925539 object centre at (A) : 14.82400 22.23500 3.292500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.083193 7.5689284E-03 midg,1,midg; midg,igrid,midg 0.3654827 -0.1433491 1,midg,midg; igrid,midg,midg 7.0776246E-02 -2.5801724E-02 gauss-seidel spectral radius is 0.9992299 estimated iterations to convergence 284 setup time was (sec) 0.9900000 now iterating at: 01:03:18 rms-change max change #iterations 8.500747 366.3768 at 10iterations 4.871617 114.7246 at 20iterations 2.768942 63.95518 at 30iterations 1.570324 32.71468 at 40iterations 0.8920971 16.80335 at 50iterations 0.5052613 10.32236 at 60iterations 0.2869169 5.379892 at 70iterations 0.1626472 3.247975 at 80iterations 9.2080563E-02 2.027755 at 90iterations 5.2247584E-02 1.004030 at 100iterations 2.9498391E-02 0.6010292 at 110iterations 1.6798481E-02 0.3463402 at 120iterations 9.5108626E-03 0.2031136 at 130iterations 5.3984765E-03 0.1035492 at 140iterations 3.0545956E-03 5.9986115E-02 at 150iterations 1.7345638E-03 3.3146858E-02 at 160iterations 9.8416884E-04 1.9363046E-02 at 170iterations 5.5804657E-04 1.1465073E-02 at 180iterations finished qdiffx linear iterations at : 01:03:29 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 5.5804657E-04 1.1465073E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 01:03:29 12.201u 0.213s 0:12.69 97.7% 0+0k 0+0io 0pf+0w