Thu Feb 2 15:34:05 PST 2012 #!/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 Thu Feb 2 2012 at 15:34:06 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 8410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.4301023 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): -11.22100 71.55000 ymin,ymax (A): -17.06800 61.78900 zmin,zma (A): -2.597000 78.05900 x,y,z range (A): 82.77100 78.85700 80.65600 scale (grids/A): 0.4301023 object centre (A): 30.16450 22.36050 37.73100 number of atom coordinates read : 8410 total number of charged atoms : 8218 net assigned charge : -1.999910 assigned positive charge : 1329.730 centred at (gu) : 89.23711 89.17798 87.58433 assigned negative charge : -1331.742 centred at (gu) : 89.23268 89.19182 87.54980 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9025 nv = 96 ne = 84 npr = 167850 no. pairs analyzed = 167850 no. exposed pairs = 10620 no. arc points = 70587 no. surface atoms = 3572 nbur = 4838 mkacc time = 0.3500000 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 = 1.960000 m= 209 mr = 4435 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 4799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5800 ## 1249 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 12447 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.7237292E-12 1.1476852E-12 midg,1,midg; midg,igrid,midg 1.0123678E-12 -1.1264379E-12 1,midg,midg; igrid,midg,midg -8.7492638E-13 1.4700963E-14 gauss-seidel spectral radius is 0.9726527 estimated iterations to convergence 50 setup time was (sec) 0.8100000 now iterating at: 15:34:07 rms-change max change #iterations 3.5563614E-02 5.318109 at 10iterations 1.8840741E-03 0.3278961 at 20iterations 7.4943184E-04 0.1246452 at 30iterations 4.0809176E-04 6.5237999E-02 at 40iterations 2.3081490E-04 3.6983490E-02 at 50iterations finished qdiffx linear iterations at : 15:34:10 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 2.3081490E-04 3.6983490E-02 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 15:34:11 4.036u 0.192s 0:04.97 84.9% 0+0k 0+47888io 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 Thu Feb 2 2012 at 15:34:11 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 8410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 1.290307 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): -11.22100 71.55000 ymin,ymax (A): -17.06800 61.78900 zmin,zma (A): -2.597000 78.05900 x,y,z range (A): 82.77100 78.85700 80.65600 scale (grids/A): 1.290307 object centre (A): 30.16450 22.36050 37.73100 number of atom coordinates read : 8410 total number of charged atoms : 8218 net assigned charge : -1.999910 assigned positive charge : 1329.730 centred at (gu) : 87.71114 87.53320 82.75199 assigned negative charge : -1331.742 centred at (gu) : 87.69882 87.57613 82.65035 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 107522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 70587 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 25914 mr = 73256 m= 1316 mr = 15580 m= 11 mr = 276 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 45651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1327 ## 34 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 56888 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) : 0.4301023 object centre at (A) : 30.16450 22.36050 37.73100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6121567E-03 3.4902475E-03 midg,1,midg; midg,igrid,midg 6.6243317E-03 -2.4887786E-04 1,midg,midg; igrid,midg,midg -1.2138121E-02 -1.7851939E-03 gauss-seidel spectral radius is 0.9975002 estimated iterations to convergence 159 setup time was (sec) 0.9100000 now iterating at: 15:34:12 rms-change max change #iterations 3.522181 142.2947 at 10iterations 1.265290 43.55781 at 20iterations 0.4535158 14.90968 at 30iterations 0.1632907 5.123672 at 40iterations 5.8788545E-02 1.872639 at 50iterations 2.1179959E-02 0.7833481 at 60iterations 7.7443821E-03 0.2754624 at 70iterations 3.0126963E-03 0.1047974 at 80iterations 1.4360300E-03 5.5156708E-02 at 90iterations 9.2682621E-04 3.2493591E-02 at 100iterations 7.1801670E-04 2.4564743E-02 at 110iterations 5.8424997E-04 1.8414259E-02 at 120iterations finished qdiffx linear iterations at : 15:34:19 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 5.8424997E-04 1.8414259E-02 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.410000 DelPhi exited at 15:34:20 8.416u 0.205s 0:09.00 95.6% 0+0k 0+46168io 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 Thu Feb 2 2012 at 15:34:20 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 8410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.935460 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): -11.22100 71.55000 ymin,ymax (A): -17.06800 61.78900 zmin,zma (A): -2.597000 78.05900 x,y,z range (A): 82.77100 78.85700 80.65600 scale (grids/A): 1.935460 object centre (A): 30.16450 22.36050 37.73100 number of atom coordinates read : 8410 total number of charged atoms : 8218 net assigned charge : -1.999910 assigned positive charge : 1329.730 centred at (gu) : 86.56656 86.29970 79.12794 assigned negative charge : -1331.742 centred at (gu) : 86.54848 86.36436 78.97575 start vw surface at 0.2100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 252721 reading accessible surface arcs data from file ARCDAT no. of arc points read = 70587 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 100619 mr = 182727 m= 18088 mr = 74940 m= 1281 mr = 11555 m= 18 mr = 487 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.610000 number of dielectric boundary points 103019 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 365 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 64773 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) : 1.290307 object centre at (A) : 30.16450 22.36050 37.73100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1427693 8.3979912E-02 midg,1,midg; midg,igrid,midg 0.2048948 -2.8162106E-04 1,midg,midg; igrid,midg,midg -0.4504701 -3.5976417E-02 gauss-seidel spectral radius is 0.9990136 estimated iterations to convergence 252 setup time was (sec) 1.850000 now iterating at: 15:34:22 rms-change max change #iterations 10.83089 285.0423 at 10iterations 5.927599 130.0670 at 20iterations 3.200647 65.84026 at 30iterations 1.725834 33.24323 at 40iterations 0.9260090 19.37423 at 50iterations 0.4946100 12.60989 at 60iterations 0.2640767 5.454212 at 70iterations 0.1405185 2.686127 at 80iterations 7.4723989E-02 1.467067 at 90iterations 3.9659895E-02 0.8538017 at 100iterations 2.1078559E-02 0.4161279 at 110iterations 1.1206502E-02 0.2251859 at 120iterations 5.9997640E-03 0.1135635 at 130iterations 3.2720312E-03 6.7951202E-02 at 140iterations 1.8432493E-03 3.9567947E-02 at 150iterations 1.1215288E-03 2.3738861E-02 at 160iterations 7.6159457E-04 1.7150879E-02 at 170iterations 5.7822326E-04 1.2493134E-02 at 180iterations finished qdiffx linear iterations at : 15:34:34 total time elapsed so far: 13.73000 # loops : 180 mean,max change (kT/e) : 5.7822326E-04 1.2493134E-02 energy calculations done at 13.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.88000 DelPhi exited at 15:34:34 13.882u 0.227s 0:14.46 97.5% 0+0k 0+46160io 0pf+0w