Mon Oct 10 12:22:44 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 12:22:44 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 = 2148 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: 0.6667916 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): -17.75900 35.63100 ymin,ymax (A): -23.65500 24.86500 zmin,zma (A): -5.328000 45.30300 x,y,z range (A): 53.39000 48.52000 50.63100 scale (grids/A): 0.6667916 object centre (A): 8.935998 0.6050005 19.98750 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999971 assigned positive charge : 322.4239 centred at (gu) : 87.29683 91.60860 86.76775 assigned negative charge : -329.4240 centred at (gu) : 87.56931 91.70695 86.70946 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6375 nv = 96 ne = 84 npr = 44372 no. pairs analyzed = 44372 no. exposed pairs = 2657 no. arc points = 18920 no. surface atoms = 902 nbur = 1246 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3434 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.2700000 number of dielectric boundary points 3233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1815 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7465 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4570997E-08 -5.7089271E-09 midg,1,midg; midg,igrid,midg -2.1736575E-09 -5.7165920E-08 1,midg,midg; igrid,midg,midg 5.4646534E-08 -4.3995399E-08 gauss-seidel spectral radius is 0.9883001 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 12:22:45 rms-change max change #iterations 0.1599706 24.00536 at 10iterations 1.7126272E-02 2.583885 at 20iterations 1.8554045E-03 0.3039069 at 30iterations 2.0347160E-04 3.0349731E-02 at 40iterations 2.1663211E-05 2.9144287E-03 at 50iterations finished qdiffx linear iterations at : 12:22:49 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 2.1663211E-05 2.9144287E-03 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 12:22:49 4.557u 0.429s 0:05.58 89.0% 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 12:22:50 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 = 2148 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: 2.000375 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): -17.75900 35.63100 ymin,ymax (A): -23.65500 24.86500 zmin,zma (A): -5.328000 45.30300 x,y,z range (A): 53.39000 48.52000 50.63100 scale (grids/A): 2.000375 object centre (A): 8.935998 0.6050005 19.98750 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999971 assigned positive charge : 322.4239 centred at (gu) : 81.89046 94.82566 80.30324 assigned negative charge : -329.4240 centred at (gu) : 82.70782 95.12073 80.12836 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 68192 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18920 grid for indexing accessible points = 1.400000 m= 24678 mr = 46426 m= 4178 mr = 18200 m= 280 mr = 2769 m= 2 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2128 time to turn everything in is 0.7100000 number of dielectric boundary points 29808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 15866 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) : 0.6667916 object centre at (A) : 8.935998 0.6050005 19.98750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5231101E-03 5.4971855E-03 midg,1,midg; midg,igrid,midg 3.4951796E-03 -1.5004472E-02 1,midg,midg; igrid,midg,midg 1.6951421E-02 -6.0204603E-02 gauss-seidel spectral radius is 0.9987013 estimated iterations to convergence 220 setup time was (sec) 1.060000 now iterating at: 12:22:51 rms-change max change #iterations 4.231987 191.3514 at 10iterations 2.020568 76.88554 at 20iterations 0.9590994 34.24162 at 30iterations 0.4590741 14.35762 at 40iterations 0.2184172 6.933935 at 50iterations 0.1040946 3.221558 at 60iterations 4.9570262E-02 1.671129 at 70iterations 2.3640202E-02 0.7620478 at 80iterations 1.1321463E-02 0.4330921 at 90iterations 5.3945822E-03 0.1747112 at 100iterations 2.5621317E-03 8.4934235E-02 at 110iterations 1.2238335E-03 3.9937973E-02 at 120iterations finished qdiffx linear iterations at : 12:23:01 total time elapsed so far: 10.96000 # loops : 120 mean,max change (kT/e) : 1.2238335E-03 3.9937973E-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) 11.14000 DelPhi exited at 12:23:02 11.141u 0.466s 0:11.90 97.4% 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 12:23:02 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 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: 3.000562 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): -17.75900 35.63100 ymin,ymax (A): -23.65500 24.86500 zmin,zma (A): -5.328000 45.30300 x,y,z range (A): 53.39000 48.52000 50.63100 scale (grids/A): 3.000562 object centre (A): 8.935998 0.6050005 19.98750 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999971 assigned positive charge : 322.4239 centred at (gu) : 77.83579 97.23850 75.45484 assigned negative charge : -329.4240 centred at (gu) : 79.06179 97.68107 75.19246 start vw surface at 0.1000000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 157545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18920 grid for indexing accessible points = 1.400000 m= 79036 mr = 112497 m= 29364 mr = 64489 m= 7686 mr = 23776 m= 1319 mr = 6072 m= 64 mr = 935 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 7205 time to turn everything in is 1.490000 number of dielectric boundary points 67216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 16056 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) : 2.000375 object centre at (A) : 8.935998 0.6050005 19.98750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7448570E-02 -8.8826371E-03 midg,1,midg; midg,igrid,midg -1.2419688E-03 -7.8418225E-02 1,midg,midg; igrid,midg,midg 0.4356124 -0.4954430 gauss-seidel spectral radius is 0.9992726 estimated iterations to convergence 293 setup time was (sec) 1.900000 now iterating at: 12:23:04 rms-change max change #iterations 9.776499 406.5211 at 10iterations 5.685052 133.9004 at 20iterations 3.304806 78.70148 at 30iterations 1.909164 40.00752 at 40iterations 1.105071 22.23104 at 50iterations 0.6371330 12.51454 at 60iterations 0.3685766 7.573987 at 70iterations 0.2125233 4.156005 at 80iterations 0.1223898 2.303284 at 90iterations 7.0606627E-02 1.286423 at 100iterations 4.0744886E-02 0.7541637 at 110iterations 2.3458110E-02 0.4063826 at 120iterations 1.3529505E-02 0.2521286 at 130iterations 7.7984645E-03 0.1398869 at 140iterations 4.4987849E-03 7.9786301E-02 at 150iterations 2.5876986E-03 4.9171448E-02 at 160iterations 1.4917251E-03 2.6615143E-02 at 170iterations 8.6287718E-04 1.5296936E-02 at 180iterations finished qdiffx linear iterations at : 12:23:20 total time elapsed so far: 17.97000 # loops : 180 mean,max change (kT/e) : 8.6287718E-04 1.5296936E-02 energy calculations done at 17.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.13000 DelPhi exited at 12:23:21 18.137u 0.548s 0:19.57 95.4% 0+0k 0+0io 0pf+0w