Mon Oct 10 14:40:06 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 Mon Oct 10 2011 at 14:40:06 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2386 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: 0.6579677 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): 17.33100 71.43700 ymin,ymax (A): 26.29000 72.31800 zmin,zma (A): 28.09700 78.19500 x,y,z range (A): 54.10600 46.02800 50.09800 scale (grids/A): 0.6579677 object centre (A): 44.38400 49.30400 53.14600 number of atom coordinates read : 2386 total number of charged atoms : 2253 net assigned charge : -2.499994 assigned positive charge : 362.6982 centred at (gu) : 90.38084 89.24862 90.22000 assigned negative charge : -365.1988 centred at (gu) : 90.17986 89.29021 90.32002 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6975 nv = 96 ne = 84 npr = 49152 no. pairs analyzed = 49152 no. exposed pairs = 2970 no. arc points = 20837 no. surface atoms = 1015 nbur = 1371 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3863 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2800000 number of dielectric boundary points 3437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2026 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8204 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0820883E-08 -2.5132801E-08 midg,1,midg; midg,igrid,midg 1.4531072E-09 -1.1568433E-08 1,midg,midg; igrid,midg,midg -3.9142058E-08 3.1084660E-08 gauss-seidel spectral radius is 0.9880116 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 14:40:07 rms-change max change #iterations 0.1620623 28.82029 at 10iterations 1.7315270E-02 2.291677 at 20iterations 1.8371778E-03 0.2610626 at 30iterations 2.1562076E-04 3.0357361E-02 at 40iterations 3.2355554E-05 4.9171448E-03 at 50iterations finished qdiffx linear iterations at : 14:40:12 total time elapsed so far: 5.090000 # loops : 50 mean,max change (kT/e) : 3.2355554E-05 4.9171448E-03 energy calculations done at 5.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.250000 DelPhi exited at 14:40:12 5.257u 0.401s 0:05.96 94.7% 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 14:40:12 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2386 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: 1.973903 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): 17.33100 71.43700 ymin,ymax (A): 26.29000 72.31800 zmin,zma (A): 28.09700 78.19500 x,y,z range (A): 54.10600 46.02800 50.09800 scale (grids/A): 1.973903 object centre (A): 44.38400 49.30400 53.14600 number of atom coordinates read : 2386 total number of charged atoms : 2253 net assigned charge : -2.499994 assigned positive charge : 362.6982 centred at (gu) : 91.14235 87.74526 90.65954 assigned negative charge : -365.1988 centred at (gu) : 90.53980 87.87067 90.95994 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75386 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20837 grid for indexing accessible points = 1.400000 m= 28159 mr = 52586 m= 5123 mr = 21071 m= 418 mr = 3349 m= 3 mr = 183 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 910 time to turn everything in is 0.6200000 number of dielectric boundary points 31900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 17816 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) : 0.6579677 object centre at (A) : 44.38400 49.30400 53.14600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8746307E-03 -3.6436975E-02 midg,1,midg; midg,igrid,midg 3.4728695E-03 -1.1534068E-02 1,midg,midg; igrid,midg,midg -7.1173073E-03 3.5096131E-02 gauss-seidel spectral radius is 0.9987087 estimated iterations to convergence 220 setup time was (sec) 0.9700000 now iterating at: 14:40:14 rms-change max change #iterations 4.448049 266.7601 at 10iterations 2.116253 70.37468 at 20iterations 1.012062 36.94240 at 30iterations 0.4840236 15.45547 at 40iterations 0.2311778 7.571053 at 50iterations 0.1104766 3.512024 at 60iterations 5.3163622E-02 1.646759 at 70iterations 2.5317814E-02 0.7871780 at 80iterations 1.2149286E-02 0.3757896 at 90iterations 5.8081369E-03 0.1860580 at 100iterations 2.7942823E-03 9.3860626E-02 at 110iterations 1.3445906E-03 4.4857025E-02 at 120iterations finished qdiffx linear iterations at : 14:40:25 total time elapsed so far: 12.40000 # loops : 120 mean,max change (kT/e) : 1.3445906E-03 4.4857025E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.56000 DelPhi exited at 14:40:25 12.561u 0.479s 0:13.32 97.8% 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 Mon Oct 10 2011 at 14:40:25 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2386 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: 2.960855 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): 17.33100 71.43700 ymin,ymax (A): 26.29000 72.31800 zmin,zma (A): 28.09700 78.19500 x,y,z range (A): 54.10600 46.02800 50.09800 scale (grids/A): 2.960855 object centre (A): 44.38400 49.30400 53.14600 number of atom coordinates read : 2386 total number of charged atoms : 2253 net assigned charge : -2.499994 assigned positive charge : 362.6982 centred at (gu) : 91.71342 86.61779 90.98917 assigned negative charge : -365.1988 centred at (gu) : 90.80960 86.80595 91.43981 start vw surface at 0.1200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 174006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20837 grid for indexing accessible points = 1.400000 m= 89531 mr = 127109 m= 34721 mr = 73964 m= 9623 mr = 28199 m= 1719 mr = 7437 m= 124 mr = 1218 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 3158 time to turn everything in is 1.670000 number of dielectric boundary points 71743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 18023 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) : 1.973903 object centre at (A) : 44.38400 49.30400 53.14600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3073120 -0.2305390 midg,1,midg; midg,igrid,midg 0.1044451 -5.0282110E-02 1,midg,midg; igrid,midg,midg 1.3301143E-03 0.4605362 gauss-seidel spectral radius is 0.9992703 estimated iterations to convergence 292 setup time was (sec) 2.040000 now iterating at: 14:40:28 rms-change max change #iterations 10.22688 456.3276 at 10iterations 5.978834 132.5354 at 20iterations 3.494006 76.68118 at 30iterations 2.039617 45.70304 at 40iterations 1.182600 26.16873 at 50iterations 0.6864327 12.13793 at 60iterations 0.3978823 7.047373 at 70iterations 0.2305145 4.495710 at 80iterations 0.1334331 2.570968 at 90iterations 7.7068299E-02 1.355726 at 100iterations 4.4601772E-02 0.8417482 at 110iterations 2.5779881E-02 0.4646149 at 120iterations 1.4870904E-02 0.2957096 at 130iterations 8.5928552E-03 0.1555576 at 140iterations 4.9786288E-03 9.0502918E-02 at 150iterations 2.8700999E-03 5.1601410E-02 at 160iterations 1.6613915E-03 2.9878616E-02 at 170iterations 9.6177304E-04 1.6448975E-02 at 180iterations finished qdiffx linear iterations at : 14:40:47 total time elapsed so far: 21.10000 # loops : 180 mean,max change (kT/e) : 9.6177304E-04 1.6448975E-02 energy calculations done at 21.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.27000 DelPhi exited at 14:40:48 21.270u 0.486s 0:22.16 98.1% 0+0k 0+0io 0pf+0w