Tue Oct 11 08:20:33 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 Tue Oct 11 2011 at 08:20:33 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 = 2104 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6877499 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): -16.31300 29.00000 ymin,ymax (A): -11.48700 36.45300 zmin,zma (A): 0.2650000 52.02800 x,y,z range (A): 45.31300 47.94000 51.76300 scale (grids/A): 0.6877499 object centre (A): 6.343500 12.48300 26.14650 number of atom coordinates read : 2104 total number of charged atoms : 2005 net assigned charge : 2.000009 assigned positive charge : 314.9715 centred at (gu) : 90.44521 89.96900 89.48292 assigned negative charge : -312.9720 centred at (gu) : 90.47046 89.99646 89.21581 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6917 nv = 96 ne = 84 npr = 42433 no. pairs analyzed = 42433 no. exposed pairs = 2793 no. arc points = 19773 no. surface atoms = 938 nbur = 1166 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 454 mr = 3789 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3000000 number of dielectric boundary points 3538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1852 ## 141 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7872 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4097557E-08 8.3886086E-08 midg,1,midg; midg,igrid,midg 1.9874216E-08 2.4097042E-09 1,midg,midg; igrid,midg,midg 1.7453454E-08 3.3581280E-09 gauss-seidel spectral radius is 0.9889982 estimated iterations to convergence 78 setup time was (sec) 0.5700000 now iterating at: 08:20:34 rms-change max change #iterations 0.1775566 27.65965 at 10iterations 2.0404806E-02 2.915852 at 20iterations 2.3779126E-03 0.3047485 at 30iterations 2.9669947E-04 4.1404724E-02 at 40iterations 4.3267464E-05 6.5059662E-03 at 50iterations finished qdiffx linear iterations at : 08:20:37 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 4.3267464E-05 6.5059662E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.010000 DelPhi exited at 08:20:38 4.013u 0.270s 0:04.67 91.6% 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 Tue Oct 11 2011 at 08:20:38 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 = 2104 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.063250 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): -16.31300 29.00000 ymin,ymax (A): -11.48700 36.45300 zmin,zma (A): 0.2650000 52.02800 x,y,z range (A): 45.31300 47.94000 51.76300 scale (grids/A): 2.063250 object centre (A): 6.343500 12.48300 26.14650 number of atom coordinates read : 2104 total number of charged atoms : 2005 net assigned charge : 2.000009 assigned positive charge : 314.9715 centred at (gu) : 91.33531 89.90684 88.44854 assigned negative charge : -312.9720 centred at (gu) : 91.41143 89.98929 87.64745 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 74069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19773 grid for indexing accessible points = 1.400000 m= 27295 mr = 50838 m= 4833 mr = 20042 m= 317 mr = 2961 m= 9 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 470 time to turn everything in is 0.6700000 number of dielectric boundary points 32596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15921 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) : 0.6877499 object centre at (A) : 6.343500 12.48300 26.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0668742E-02 7.0154369E-02 midg,1,midg; midg,igrid,midg 1.0239819E-02 -3.1810813E-02 1,midg,midg; igrid,midg,midg 1.2104204E-02 -9.0807434E-03 gauss-seidel spectral radius is 0.9987885 estimated iterations to convergence 227 setup time was (sec) 0.9700000 now iterating at: 08:20:39 rms-change max change #iterations 4.344384 185.6736 at 10iterations 2.107339 67.57474 at 20iterations 1.036555 33.93255 at 30iterations 0.5069022 14.96193 at 40iterations 0.2482911 8.176045 at 50iterations 0.1209302 3.801883 at 60iterations 5.9298605E-02 1.763786 at 70iterations 2.9080639E-02 0.8794365 at 80iterations 1.4253275E-02 0.4578400 at 90iterations 6.9499505E-03 0.2258930 at 100iterations 3.4155503E-03 0.1083317 at 110iterations 1.6713106E-03 4.9316406E-02 at 120iterations finished qdiffx linear iterations at : 08:20:47 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 1.6713106E-03 4.9316406E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 08:20:48 9.466u 0.292s 0:10.34 94.2% 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 Tue Oct 11 2011 at 08:20:48 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 = 2104 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.094875 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): -16.31300 29.00000 ymin,ymax (A): -11.48700 36.45300 zmin,zma (A): 0.2650000 52.02800 x,y,z range (A): 45.31300 47.94000 51.76300 scale (grids/A): 3.094875 object centre (A): 6.343500 12.48300 26.14650 number of atom coordinates read : 2104 total number of charged atoms : 2005 net assigned charge : 2.000009 assigned positive charge : 314.9715 centred at (gu) : 92.00284 89.86019 87.67279 assigned negative charge : -312.9720 centred at (gu) : 92.11716 89.98395 86.47115 start vw surface at 0.1500000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 171131 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19773 grid for indexing accessible points = 1.400000 m= 86409 mr = 123293 m= 33557 mr = 70325 m= 8710 mr = 26751 m= 1338 mr = 6462 m= 97 mr = 761 m= 11 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1546 time to turn everything in is 2.140000 number of dielectric boundary points 73623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 16040 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) : 2.063250 object centre at (A) : 6.343500 12.48300 26.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7658237 0.7589703 midg,1,midg; midg,igrid,midg 0.1356629 -0.3090353 1,midg,midg; igrid,midg,midg 9.4446592E-02 -0.1180030 gauss-seidel spectral radius is 0.9993021 estimated iterations to convergence 299 setup time was (sec) 2.480000 now iterating at: 08:20:51 rms-change max change #iterations 10.00391 456.0104 at 10iterations 5.911146 134.3174 at 20iterations 3.491271 73.46744 at 30iterations 2.062653 41.85450 at 40iterations 1.216935 25.43463 at 50iterations 0.7124962 13.66100 at 60iterations 0.4185062 7.143768 at 70iterations 0.2445898 5.183632 at 80iterations 0.1435278 2.676256 at 90iterations 8.3963640E-02 1.428642 at 100iterations 4.9193960E-02 0.9326172 at 110iterations 2.8643539E-02 0.5081100 at 120iterations 1.6756412E-02 0.2965574 at 130iterations 9.8010227E-03 0.1766586 at 140iterations 5.7164249E-03 9.5788956E-02 at 150iterations 3.3452294E-03 5.9101105E-02 at 160iterations 1.9528285E-03 3.6284924E-02 at 170iterations 1.1422246E-03 2.2919655E-02 at 180iterations finished qdiffx linear iterations at : 08:21:05 total time elapsed so far: 16.24000 # loops : 180 mean,max change (kT/e) : 1.1422246E-03 2.2919655E-02 energy calculations done at 16.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.42000 DelPhi exited at 08:21:05 16.420u 0.278s 0:16.99 98.2% 0+0k 0+0io 0pf+0w