Mon Oct 10 11:33:37 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 11:33:37 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 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: 0.6710650 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): -22.23400 24.90900 ymin,ymax (A): -21.14400 26.40700 zmin,zma (A): -16.75600 36.29400 x,y,z range (A): 47.14300 47.55100 53.05000 scale (grids/A): 0.6710650 object centre (A): 1.337501 2.631500 9.768999 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -7.999972 assigned positive charge : 320.1319 centred at (gu) : 91.95815 88.63407 92.17527 assigned negative charge : -328.1320 centred at (gu) : 92.06461 88.57873 91.92380 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6364 nv = 96 ne = 84 npr = 44704 no. pairs analyzed = 44704 no. exposed pairs = 2682 no. arc points = 18879 no. surface atoms = 902 nbur = 1234 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3439 m= 0 mr = 44 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2900000 number of dielectric boundary points 3235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1691 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7320 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4033976E-08 4.2321968E-08 midg,1,midg; midg,igrid,midg -5.2405706E-08 -1.2017338E-08 1,midg,midg; igrid,midg,midg -3.4340313E-09 -7.6399125E-08 gauss-seidel spectral radius is 0.9884442 estimated iterations to convergence 76 setup time was (sec) 0.5500000 now iterating at: 11:33:38 rms-change max change #iterations 0.1622889 29.54181 at 10iterations 1.8020047E-02 2.473318 at 20iterations 1.9571809E-03 0.2676086 at 30iterations 2.1147747E-04 2.9767036E-02 at 40iterations 2.3487779E-05 3.5426617E-03 at 50iterations finished qdiffx linear iterations at : 11:33:41 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 2.3487779E-05 3.5426617E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 11:33:41 3.610u 0.206s 0:04.11 92.7% 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 11:33:42 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.013195 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): -22.23400 24.90900 ymin,ymax (A): -21.14400 26.40700 zmin,zma (A): -16.75600 36.29400 x,y,z range (A): 47.14300 47.55100 53.05000 scale (grids/A): 2.013195 object centre (A): 1.337501 2.631500 9.768999 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -7.999972 assigned positive charge : 320.1319 centred at (gu) : 95.87440 85.90222 96.52571 assigned negative charge : -328.1320 centred at (gu) : 96.19402 85.73622 95.77133 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67470 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18879 grid for indexing accessible points = 1.400000 m= 24067 mr = 45852 m= 3958 mr = 17501 m= 258 mr = 2509 m= 7 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1016 time to turn everything in is 0.5400000 number of dielectric boundary points 29802 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15772 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) : 0.6710650 object centre at (A) : 1.337501 2.631500 9.768999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5433544E-02 -3.7367947E-03 midg,1,midg; midg,igrid,midg -1.4988571E-02 1.0186883E-03 1,midg,midg; igrid,midg,midg -1.1067940E-02 -4.9542367E-02 gauss-seidel spectral radius is 0.9987191 estimated iterations to convergence 221 setup time was (sec) 0.8700000 now iterating at: 11:33:43 rms-change max change #iterations 4.229033 222.5694 at 10iterations 2.033779 80.16354 at 20iterations 0.9680610 35.85606 at 30iterations 0.4649485 15.70489 at 40iterations 0.2223475 7.055252 at 50iterations 0.1064320 3.722054 at 60iterations 5.1165618E-02 1.882784 at 70iterations 2.4497425E-02 0.8003616 at 80iterations 1.1742442E-02 0.3924732 at 90iterations 5.6273928E-03 0.1885910 at 100iterations 2.6927604E-03 9.0459824E-02 at 110iterations 1.2950444E-03 4.0509224E-02 at 120iterations finished qdiffx linear iterations at : 11:33:50 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 1.2950444E-03 4.0509224E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 11:33:50 8.070u 0.232s 0:08.73 95.0% 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 11:33:50 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 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: 3.019793 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): -22.23400 24.90900 ymin,ymax (A): -21.14400 26.40700 zmin,zma (A): -16.75600 36.29400 x,y,z range (A): 47.14300 47.55100 53.05000 scale (grids/A): 3.019793 object centre (A): 1.337501 2.631500 9.768999 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -7.999972 assigned positive charge : 320.1319 centred at (gu) : 98.81145 83.85331 99.78850 assigned negative charge : -328.1320 centred at (gu) : 99.29099 83.60426 98.65691 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 155900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18879 grid for indexing accessible points = 1.400000 m= 77487 mr = 111064 m= 28179 mr = 62954 m= 7226 mr = 22484 m= 1169 mr = 5473 m= 112 mr = 798 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 3612 time to turn everything in is 1.320000 number of dielectric boundary points 67241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 15960 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) : 2.013195 object centre at (A) : 1.337501 2.631500 9.768999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3245330 6.3030280E-02 midg,1,midg; midg,igrid,midg -8.3682127E-02 -1.2874816E-02 1,midg,midg; igrid,midg,midg -0.1386863 -0.4210100 gauss-seidel spectral radius is 0.9992760 estimated iterations to convergence 293 setup time was (sec) 1.640000 now iterating at: 11:33:52 rms-change max change #iterations 9.869934 428.9378 at 10iterations 5.748583 127.1225 at 20iterations 3.340877 73.97627 at 30iterations 1.936879 40.89032 at 40iterations 1.122445 22.18351 at 50iterations 0.6487247 12.58303 at 60iterations 0.3749700 7.568628 at 70iterations 0.2166573 4.063004 at 80iterations 0.1251972 2.513048 at 90iterations 7.2003260E-02 1.294268 at 100iterations 4.1655608E-02 0.7793655 at 110iterations 2.4060782E-02 0.4439435 at 120iterations 1.3871455E-02 0.2702789 at 130iterations 8.0354270E-03 0.1474857 at 140iterations 4.6304781E-03 9.4184130E-02 at 150iterations 2.6707654E-03 4.7794342E-02 at 160iterations 1.5409779E-03 2.7046204E-02 at 170iterations 8.9082395E-04 1.8194199E-02 at 180iterations finished qdiffx linear iterations at : 11:34:03 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 8.9082395E-04 1.8194199E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 11:34:03 12.632u 0.227s 0:13.16 97.6% 0+0k 0+0io 0pf+0w