Sun Oct 9 12:38:02 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 Sun Oct 9 2011 at 12:38:02 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 = 2383 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: 0.6748687 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): -5.601000 44.28400 ymin,ymax (A): -14.14600 38.60500 zmin,zma (A): 2.912000 45.54600 x,y,z range (A): 49.88499 52.75100 42.63400 scale (grids/A): 0.6748687 object centre (A): 19.34150 12.22950 24.22900 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 363.7711 centred at (gu) : 89.48123 90.48457 90.27105 assigned negative charge : -359.2716 centred at (gu) : 89.46359 90.63988 90.33035 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7312 nv = 96 ne = 84 npr = 47671 no. pairs analyzed = 47671 no. exposed pairs = 3074 no. arc points = 21306 no. surface atoms = 1019 nbur = 1364 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 440 mr = 3979 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2063 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8395 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1202376E-08 1.4616076E-09 midg,1,midg; midg,igrid,midg 5.2458699E-08 -2.7398755E-08 1,midg,midg; igrid,midg,midg 1.3922622E-08 1.9823291E-08 gauss-seidel spectral radius is 0.9885976 estimated iterations to convergence 76 setup time was (sec) 0.4800000 now iterating at: 12:38:03 rms-change max change #iterations 0.1725697 29.92582 at 10iterations 1.9451555E-02 2.473680 at 20iterations 2.6245296E-03 0.4386787 at 30iterations 5.6900870E-04 9.9884033E-02 at 40iterations 1.7430980E-04 2.9945374E-02 at 50iterations finished qdiffx linear iterations at : 12:38:05 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 1.7430980E-04 2.9945374E-02 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 12:38:06 3.036u 0.146s 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 12:38:06 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.024606 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): -5.601000 44.28400 ymin,ymax (A): -14.14600 38.60500 zmin,zma (A): 2.912000 45.54600 x,y,z range (A): 49.88499 52.75100 42.63400 scale (grids/A): 2.024606 object centre (A): 19.34150 12.22950 24.22900 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 363.7711 centred at (gu) : 88.44319 91.45326 90.81264 assigned negative charge : -359.2716 centred at (gu) : 88.39054 91.91943 90.99082 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78071 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21306 grid for indexing accessible points = 1.400000 m= 29963 mr = 53966 m= 4998 mr = 22058 m= 400 mr = 3092 m= 2 mr = 173 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 34145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17715 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) : 0.6748687 object centre at (A) : 19.34150 12.22950 24.22900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1769769E-02 9.6659251E-03 midg,1,midg; midg,igrid,midg 1.8676402E-02 -2.9940989E-02 1,midg,midg; igrid,midg,midg 3.3761069E-02 4.5792065E-03 gauss-seidel spectral radius is 0.9987700 estimated iterations to convergence 226 setup time was (sec) 0.8300000 now iterating at: 12:38:07 rms-change max change #iterations 4.606095 219.7373 at 10iterations 2.224618 79.58247 at 20iterations 1.085533 32.96680 at 30iterations 0.5271195 15.32653 at 40iterations 0.2559711 7.773417 at 50iterations 0.1248767 3.812010 at 60iterations 6.1068848E-02 1.808300 at 70iterations 2.9748432E-02 0.8716774 at 80iterations 1.4671915E-02 0.4042082 at 90iterations 7.2297696E-03 0.2099118 at 100iterations 3.6337583E-03 0.1087379 at 110iterations 1.8927420E-03 6.0302734E-02 at 120iterations finished qdiffx linear iterations at : 12:38:13 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 1.8927420E-03 6.0302734E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 12:38:13 6.950u 0.167s 0:07.39 96.2% 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 Sun Oct 9 2011 at 12:38:13 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 = 2383 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: 3.036909 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): -5.601000 44.28400 ymin,ymax (A): -14.14600 38.60500 zmin,zma (A): 2.912000 45.54600 x,y,z range (A): 49.88499 52.75100 42.63400 scale (grids/A): 3.036909 object centre (A): 19.34150 12.22950 24.22900 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 363.7711 centred at (gu) : 87.66462 92.17973 91.21882 assigned negative charge : -359.2716 centred at (gu) : 87.58582 92.87914 91.48616 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 179908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21306 grid for indexing accessible points = 1.400000 m= 94512 mr = 130196 m= 36000 mr = 77282 m= 9034 mr = 28861 m= 1586 mr = 6689 m= 123 mr = 1102 m= 3 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 76974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 17934 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) : 2.024606 object centre at (A) : 19.34150 12.22950 24.22900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3912823 9.2709279E-03 midg,1,midg; midg,igrid,midg 0.4569823 -0.3866710 1,midg,midg; igrid,midg,midg 0.3636165 -0.1332078 gauss-seidel spectral radius is 0.9992844 estimated iterations to convergence 295 setup time was (sec) 1.660000 now iterating at: 12:38:15 rms-change max change #iterations 10.48643 407.2404 at 10iterations 6.171455 149.0209 at 20iterations 3.639822 88.40244 at 30iterations 2.140672 42.18751 at 40iterations 1.254713 26.28687 at 50iterations 0.7330777 14.93972 at 60iterations 0.4290519 7.754424 at 70iterations 0.2502656 4.412249 at 80iterations 0.1459377 2.839205 at 90iterations 8.5098647E-02 1.513983 at 100iterations 4.9728267E-02 0.8778683 at 110iterations 2.9095881E-02 0.5987740 at 120iterations 1.7149154E-02 0.3223915 at 130iterations 1.0202454E-02 0.1797562 at 140iterations 6.2215626E-03 0.1225128 at 150iterations 3.9280187E-03 8.5197449E-02 at 160iterations 2.6233192E-03 5.8654785E-02 at 170iterations 1.8638126E-03 4.1572571E-02 at 180iterations finished qdiffx linear iterations at : 12:38:24 total time elapsed so far: 10.96000 # loops : 180 mean,max change (kT/e) : 1.8638126E-03 4.1572571E-02 energy calculations done at 10.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 12:38:25 11.126u 0.181s 0:11.56 97.7% 0+0k 0+0io 0pf+0w