Sun Oct 9 07:43:19 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 07:43:19 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 = 1961 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5749911 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): 1.083000 62.99700 ymin,ymax (A): -20.66600 23.62900 zmin,zma (A): -15.61100 35.00500 x,y,z range (A): 61.91400 44.29500 50.61600 scale (grids/A): 0.5749911 object centre (A): 32.04000 1.481500 9.697001 number of atom coordinates read : 1961 total number of charged atoms : 1822 net assigned charge : -7.499987 assigned positive charge : 290.5220 centred at (gu) : 87.17146 90.10420 90.28124 assigned negative charge : -298.0218 centred at (gu) : 86.96294 89.72431 90.13869 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4390 nv = 96 ne = 84 npr = 38369 no. pairs analyzed = 38369 no. exposed pairs = 2764 no. arc points = 20207 no. surface atoms = 930 nbur = 1031 mkacc time = 7.9999998E-02 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 = 1.512000 m= 201 mr = 2084 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2501 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2066 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 5504 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8700391E-09 4.8948562E-10 midg,1,midg; midg,igrid,midg -6.0335688E-09 3.2869858E-09 1,midg,midg; igrid,midg,midg -7.7317308E-09 6.1064082E-10 gauss-seidel spectral radius is 0.9843172 estimated iterations to convergence 66 setup time was (sec) 0.4600000 now iterating at: 07:43:20 rms-change max change #iterations 7.5711191E-02 15.05575 at 10iterations 5.5646859E-03 1.191697 at 20iterations 4.2390256E-04 7.3525429E-02 at 30iterations 3.1739466E-05 5.4321289E-03 at 40iterations 2.3694222E-06 4.8351288E-04 at 50iterations finished qdiffx linear iterations at : 07:43:22 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 2.3694222E-06 4.8351288E-04 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 07:43:23 3.043u 0.138s 0:03.45 91.8% 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 Sun Oct 9 2011 at 07:43:23 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1961 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.724973 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): 1.083000 62.99700 ymin,ymax (A): -20.66600 23.62900 zmin,zma (A): -15.61100 35.00500 x,y,z range (A): 61.91400 44.29500 50.61600 scale (grids/A): 1.724973 object centre (A): 32.04000 1.481500 9.697001 number of atom coordinates read : 1961 total number of charged atoms : 1822 net assigned charge : -7.499987 assigned positive charge : 290.5220 centred at (gu) : 81.51434 90.31222 90.84367 assigned negative charge : -298.0218 centred at (gu) : 80.88891 89.17290 90.41585 start vw surface at 0.2000000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 47351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20207 grid for indexing accessible points = 1.400000 m= 14341 mr = 29545 m= 1464 mr = 9769 m= 43 mr = 714 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 366 time to turn everything in is 0.4300000 number of dielectric boundary points 23167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14128 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) : 0.5749911 object centre at (A) : 32.04000 1.481500 9.697001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1885878E-02 9.1456948E-04 midg,1,midg; midg,igrid,midg -2.5626201E-02 4.5091980E-03 1,midg,midg; igrid,midg,midg -5.5913500E-02 2.2118236E-03 gauss-seidel spectral radius is 0.9982728 estimated iterations to convergence 191 setup time was (sec) 0.6800000 now iterating at: 07:43:23 rms-change max change #iterations 2.961016 168.1725 at 10iterations 1.247902 53.94426 at 20iterations 0.5302480 21.79284 at 30iterations 0.2250639 10.43111 at 40iterations 9.5756151E-02 3.888531 at 50iterations 4.0551238E-02 1.701660 at 60iterations 1.7218061E-02 0.6920357 at 70iterations 7.3150019E-03 0.2845058 at 80iterations 3.1134922E-03 0.1307774 at 90iterations 1.3181965E-03 5.7998657E-02 at 100iterations 5.5923511E-04 2.4562836E-02 at 110iterations 2.3829790E-04 9.7179413E-03 at 120iterations finished qdiffx linear iterations at : 07:43:29 total time elapsed so far: 6.570000 # loops : 120 mean,max change (kT/e) : 2.3829790E-04 9.7179413E-03 energy calculations done at 6.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.750000 DelPhi exited at 07:43:30 6.748u 0.194s 0:07.23 95.8% 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 Sun Oct 9 2011 at 07:43:30 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1961 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: 2.587460 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): 1.083000 62.99700 ymin,ymax (A): -20.66600 23.62900 zmin,zma (A): -15.61100 35.00500 x,y,z range (A): 61.91400 44.29500 50.61600 scale (grids/A): 2.587460 object centre (A): 32.04000 1.481500 9.697001 number of atom coordinates read : 1961 total number of charged atoms : 1822 net assigned charge : -7.499987 assigned positive charge : 290.5220 centred at (gu) : 77.27156 90.46839 91.26543 assigned negative charge : -298.0218 centred at (gu) : 76.33328 88.75934 90.62370 start vw surface at 0.1400000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 109724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20207 grid for indexing accessible points = 1.400000 m= 48779 mr = 72861 m= 14252 mr = 37757 m= 2321 mr = 10713 m= 172 mr = 1542 m= 2 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1232 time to turn everything in is 0.8100000 number of dielectric boundary points 52293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 14573 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) : 1.724973 object centre at (A) : 32.04000 1.481500 9.697001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1268972 -1.1328375E-02 midg,1,midg; midg,igrid,midg -0.3351734 5.0220408E-02 1,midg,midg; igrid,midg,midg -0.6171342 4.9666297E-02 gauss-seidel spectral radius is 0.9991488 estimated iterations to convergence 271 setup time was (sec) 1.080000 now iterating at: 07:43:31 rms-change max change #iterations 7.473288 255.5807 at 10iterations 4.206427 120.9055 at 20iterations 2.340556 73.98320 at 30iterations 1.301765 34.76189 at 40iterations 0.7205459 18.27433 at 50iterations 0.3996460 10.14985 at 60iterations 0.2208374 5.143272 at 70iterations 0.1216986 3.025986 at 80iterations 6.7016713E-02 1.643343 at 90iterations 3.7001565E-02 0.7956657 at 100iterations 2.0397002E-02 0.5071487 at 110iterations 1.1225027E-02 0.2621078 at 120iterations 6.1772522E-03 0.1424274 at 130iterations 3.4071717E-03 7.6733589E-02 at 140iterations 1.8661700E-03 4.3315709E-02 at 150iterations 1.0295730E-03 2.3685455E-02 at 160iterations 5.6696276E-04 1.2607574E-02 at 170iterations 3.1135825E-04 7.4033737E-03 at 180iterations finished qdiffx linear iterations at : 07:43:41 total time elapsed so far: 11.13000 # loops : 180 mean,max change (kT/e) : 3.1135825E-04 7.4033737E-03 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.32000 DelPhi exited at 07:43:42 11.322u 0.218s 0:11.82 97.5% 0+0k 0+0io 0pf+0w