Mon Oct 10 17:04:16 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 17:04:16 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2729 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 0.5475659 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): 0.9060000 50.86800 ymin,ymax (A): -6.303000 45.78300 zmin,zma (A): 14.86900 79.88400 x,y,z range (A): 49.96200 52.08600 65.01500 scale (grids/A): 0.5475659 object centre (A): 25.88700 19.74000 47.37650 number of atom coordinates read : 2729 total number of charged atoms : 2585 net assigned charge : 3.906018 assigned positive charge : 407.7177 centred at (gu) : 89.88316 88.81567 90.83674 assigned negative charge : -403.8126 centred at (gu) : 89.97303 88.92728 90.83937 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5025 nv = 96 ne = 84 npr = 56119 no. pairs analyzed = 56119 no. exposed pairs = 3425 no. arc points = 24436 no. surface atoms = 1161 nbur = 1568 mkacc time = 0.1300000 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 = 1.540000 m= 200 mr = 2454 m= 0 mr = 8 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.3100000 number of dielectric boundary points 2763 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2451 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6751 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1755568E-10 2.8338534E-10 midg,1,midg; midg,igrid,midg 1.2803519E-09 -3.5071937E-10 1,midg,midg; igrid,midg,midg 8.4103502E-10 -3.2243799E-10 gauss-seidel spectral radius is 0.9827807 estimated iterations to convergence 63 setup time was (sec) 0.5500000 now iterating at: 17:04:17 rms-change max change #iterations 6.9707699E-02 12.48829 at 10iterations 4.7340509E-03 0.8012772 at 20iterations 3.1558610E-04 5.5395126E-02 at 30iterations 2.1512098E-05 3.6067963E-03 at 40iterations 1.5343020E-06 2.9277802E-04 at 50iterations finished qdiffx linear iterations at : 17:04:20 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.5343020E-06 2.9277802E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 17:04:22 3.440u 0.233s 0:05.26 69.7% 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 17:04:22 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2729 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.642698 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): 0.9060000 50.86800 ymin,ymax (A): -6.303000 45.78300 zmin,zma (A): 14.86900 79.88400 x,y,z range (A): 49.96200 52.08600 65.01500 scale (grids/A): 1.642698 object centre (A): 25.88700 19.74000 47.37650 number of atom coordinates read : 2729 total number of charged atoms : 2585 net assigned charge : 3.906018 assigned positive charge : 407.7177 centred at (gu) : 89.64871 86.44654 92.50976 assigned negative charge : -403.8126 centred at (gu) : 89.91897 86.78171 92.51783 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 55665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24436 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15457 mr = 36314 m= 1493 mr = 10096 m= 38 mr = 682 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 526 time to turn everything in is 0.4700000 number of dielectric boundary points 25561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 267 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19837 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) : 0.5475659 object centre at (A) : 25.88700 19.74000 47.37650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1306012E-02 -3.4556590E-02 midg,1,midg; midg,igrid,midg 1.9885596E-02 -2.1439229E-04 1,midg,midg; igrid,midg,midg 5.2509280E-03 -3.4220873E-03 gauss-seidel spectral radius is 0.9981714 estimated iterations to convergence 186 setup time was (sec) 0.7800000 now iterating at: 17:04:23 rms-change max change #iterations 3.181672 184.1378 at 10iterations 1.314466 57.79618 at 20iterations 0.5475305 22.65508 at 30iterations 0.2252615 8.692752 at 40iterations 9.4024234E-02 3.537889 at 50iterations 3.8975291E-02 1.398712 at 60iterations 1.6165160E-02 0.6878843 at 70iterations 6.7228209E-03 0.2672634 at 80iterations 2.7913288E-03 0.1261730 at 90iterations 1.1637419E-03 4.4219017E-02 at 100iterations 4.8271508E-04 1.8104553E-02 at 110iterations 2.0117800E-04 6.9923401E-03 at 120iterations finished qdiffx linear iterations at : 17:04:30 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 2.0117800E-04 6.9923401E-03 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 17:04:30 7.936u 0.236s 0:08.60 94.8% 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 17:04:30 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2729 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 2.464047 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): 0.9060000 50.86800 ymin,ymax (A): -6.303000 45.78300 zmin,zma (A): 14.86900 79.88400 x,y,z range (A): 49.96200 52.08600 65.01500 scale (grids/A): 2.464047 object centre (A): 25.88700 19.74000 47.37650 number of atom coordinates read : 2729 total number of charged atoms : 2585 net assigned charge : 3.906018 assigned positive charge : 407.7177 centred at (gu) : 89.47305 84.66965 93.76466 assigned negative charge : -403.8126 centred at (gu) : 89.87847 85.17251 93.77676 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 129477 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24436 grid for indexing accessible points = 1.400000 m= 53855 mr = 89419 m= 14458 mr = 41086 m= 2242 mr = 10607 m= 157 mr = 1398 m= 3 mr = 50 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1836 time to turn everything in is 1.020000 number of dielectric boundary points 57633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 20654 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) : 1.642698 object centre at (A) : 25.88700 19.74000 47.37650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2297656 -0.7881159 midg,1,midg; midg,igrid,midg 0.3153403 -4.6630107E-02 1,midg,midg; igrid,midg,midg 6.0338583E-02 -4.5288190E-02 gauss-seidel spectral radius is 0.9991260 estimated iterations to convergence 267 setup time was (sec) 1.330000 now iterating at: 17:04:32 rms-change max change #iterations 8.213029 286.0702 at 10iterations 4.575594 123.2150 at 20iterations 2.526070 67.39420 at 30iterations 1.399611 32.06657 at 40iterations 0.7692779 21.41004 at 50iterations 0.4227890 9.310860 at 60iterations 0.2320923 5.336488 at 70iterations 0.1271030 2.832693 at 80iterations 6.9495484E-02 1.597839 at 90iterations 3.8047601E-02 0.8265457 at 100iterations 2.0808579E-02 0.4669800 at 110iterations 1.1370924E-02 0.2437586 at 120iterations 6.2126410E-03 0.1413460 at 130iterations 3.3986457E-03 7.5334549E-02 at 140iterations 1.8566947E-03 4.2399406E-02 at 150iterations 1.0169087E-03 2.1110535E-02 at 160iterations 5.5473077E-04 1.2573242E-02 at 170iterations 3.0299611E-04 7.0819855E-03 at 180iterations finished qdiffx linear iterations at : 17:04:43 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 3.0299611E-04 7.0819855E-03 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 17:04:44 12.435u 0.266s 0:13.95 90.9% 0+0k 0+0io 0pf+0w