Sun Oct 9 08:17:11 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 Sun Oct 9 2011 at 08:17:11 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 # of charge parameter records: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4893 !!! WARNING: HIR 702 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5206886 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): 46.50600 114.8770 ymin,ymax (A): 40.33900 105.1660 zmin,zma (A): 70.77200 132.5430 x,y,z range (A): 68.37100 64.82700 61.77100 scale (grids/A): 0.5206886 object centre (A): 80.69150 72.75250 101.6575 number of atom coordinates read : 4893 total number of charged atoms : 4733 net assigned charge : -2.985990 assigned positive charge : 746.1629 centred at (gu) : 91.15503 91.54221 89.59347 assigned negative charge : -749.1544 centred at (gu) : 91.23894 91.55523 89.52173 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8433 nv = 96 ne = 84 npr = 97880 no. pairs analyzed = 97880 no. exposed pairs = 6242 no. arc points = 43355 no. surface atoms = 2101 nbur = 2792 mkacc time = 0.2100000 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 = 1.652000 m= 303 mr = 4292 m= 0 mr = 7 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.4700000 number of dielectric boundary points 4437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4337 ## 639 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11291 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9813502E-10 2.1102244E-10 midg,1,midg; midg,igrid,midg -4.0985592E-12 -1.6766676E-10 1,midg,midg; igrid,midg,midg 2.0970514E-10 -5.5460236E-10 gauss-seidel spectral radius is 0.9811451 estimated iterations to convergence 60 setup time was (sec) 0.6900000 now iterating at: 08:17:12 rms-change max change #iterations 7.5880758E-02 10.05411 at 10iterations 5.0926753E-03 0.8056221 at 20iterations 6.8536162E-04 0.1804771 at 30iterations 1.9848473E-04 5.3005219E-02 at 40iterations 6.4805274E-05 1.6345978E-02 at 50iterations finished qdiffx linear iterations at : 08:17:14 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 6.4805274E-05 1.6345978E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 08:17:15 3.278u 0.136s 0:03.72 91.3% 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 Sun Oct 9 2011 at 08:17:15 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4893 !!! WARNING: HIR 702 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.562066 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): 46.50600 114.8770 ymin,ymax (A): 40.33900 105.1660 zmin,zma (A): 70.77200 132.5430 x,y,z range (A): 68.37100 64.82700 61.77100 scale (grids/A): 1.562066 object centre (A): 80.69150 72.75250 101.6575 number of atom coordinates read : 4893 total number of charged atoms : 4733 net assigned charge : -2.985990 assigned positive charge : 746.1629 centred at (gu) : 93.46327 94.62508 88.77831 assigned negative charge : -749.1544 centred at (gu) : 93.71633 94.66521 88.56470 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 93890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43355 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 27808 mr = 63458 m= 2645 mr = 18556 m= 62 mr = 1311 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 526 time to turn everything in is 0.6400000 number of dielectric boundary points 41080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 623 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 35839 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) : 0.5206886 object centre at (A) : 80.69150 72.75250 101.6575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9533954E-03 -4.6069631E-03 midg,1,midg; midg,igrid,midg -6.4500319E-03 -2.7669806E-03 1,midg,midg; igrid,midg,midg 1.0052759E-03 -1.0120030E-02 gauss-seidel spectral radius is 0.9982123 estimated iterations to convergence 188 setup time was (sec) 0.9200000 now iterating at: 08:17:16 rms-change max change #iterations 4.066204 176.0399 at 10iterations 1.709006 57.18777 at 20iterations 0.7184775 27.13900 at 30iterations 0.3012160 10.42944 at 40iterations 0.1271030 4.282825 at 50iterations 5.3457025E-02 1.682039 at 60iterations 2.2585431E-02 0.7042189 at 70iterations 9.5100766E-03 0.2927710 at 80iterations 4.0263757E-03 0.1194305 at 90iterations 1.7182556E-03 5.8269501E-02 at 100iterations 7.4211194E-04 2.5238037E-02 at 110iterations 3.3040281E-04 1.1627197E-02 at 120iterations finished qdiffx linear iterations at : 08:17:22 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 3.3040281E-04 1.1627197E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 08:17:23 7.127u 0.144s 0:07.55 96.1% 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 Sun Oct 9 2011 at 08:17:23 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4893 !!! WARNING: HIR 702 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.343099 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): 46.50600 114.8770 ymin,ymax (A): 40.33900 105.1660 zmin,zma (A): 70.77200 132.5430 x,y,z range (A): 68.37100 64.82700 61.77100 scale (grids/A): 2.343099 object centre (A): 80.69150 72.75250 101.6575 number of atom coordinates read : 4893 total number of charged atoms : 4733 net assigned charge : -2.985990 assigned positive charge : 746.1629 centred at (gu) : 95.19419 96.93723 88.16711 assigned negative charge : -749.1544 centred at (gu) : 95.57444 96.99755 87.84686 start vw surface at 0.1900000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 218518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43355 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 97750 mr = 156178 m= 26298 mr = 75524 m= 4022 mr = 19538 m= 212 mr = 2646 m= 4 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1786 time to turn everything in is 1.520000 number of dielectric boundary points 92824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 37771 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) : 1.562066 object centre at (A) : 80.69150 72.75250 101.6575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2297859 -0.2441905 midg,1,midg; midg,igrid,midg -0.1203737 -0.1321794 1,midg,midg; igrid,midg,midg 3.8682964E-02 -9.2253881E-03 gauss-seidel spectral radius is 0.9992063 estimated iterations to convergence 280 setup time was (sec) 1.810000 now iterating at: 08:17:25 rms-change max change #iterations 11.03945 314.0543 at 10iterations 6.486757 157.7974 at 20iterations 3.767416 78.53569 at 30iterations 2.181728 48.53217 at 40iterations 1.254430 26.94357 at 50iterations 0.7208200 15.13000 at 60iterations 0.4126260 8.077377 at 70iterations 0.2352905 4.529365 at 80iterations 0.1338904 2.603910 at 90iterations 7.6039895E-02 1.464249 at 100iterations 4.3162420E-02 0.7799854 at 110iterations 2.4534445E-02 0.4637928 at 120iterations 1.3905434E-02 0.2496204 at 130iterations 7.8807883E-03 0.1571732 at 140iterations 4.4729766E-03 8.5142136E-02 at 150iterations 2.5324745E-03 5.0262779E-02 at 160iterations 1.4409516E-03 2.5966644E-02 at 170iterations 8.2087435E-04 1.4280796E-02 at 180iterations finished qdiffx linear iterations at : 08:17:34 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 8.2087435E-04 1.4280796E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 08:17:35 11.553u 0.166s 0:12.01 97.5% 0+0k 0+0io 0pf+0w