Sun Oct 9 14:51:03 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 14:51:03 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 = 1866 !!! WARNING: GLU 107 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6539189 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): -17.89700 36.54400 ymin,ymax (A): -19.83700 28.78000 zmin,zma (A): -19.06800 31.19900 x,y,z range (A): 54.44100 48.61700 50.26700 scale (grids/A): 0.6539189 object centre (A): 9.323500 4.471499 6.065501 number of atom coordinates read : 1866 total number of charged atoms : 1731 net assigned charge : 1.500004 assigned positive charge : 276.1492 centred at (gu) : 88.80112 89.00983 90.54915 assigned negative charge : -274.6493 centred at (gu) : 88.81876 89.22570 90.57502 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5709 nv = 96 ne = 84 npr = 35759 no. pairs analyzed = 35759 no. exposed pairs = 2608 no. arc points = 18910 no. surface atoms = 882 nbur = 984 mkacc time = 5.9999995E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 2847 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.1400000 number of dielectric boundary points 3134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1808 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.2000000 number of grid points assigned charge 6354 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3887756E-09 -1.8149571E-10 midg,1,midg; midg,igrid,midg 3.4783916E-08 -1.8934326E-08 1,midg,midg; igrid,midg,midg 6.4935115E-09 6.9207035E-10 gauss-seidel spectral radius is 0.9878278 estimated iterations to convergence 74 setup time was (sec) 0.3200000 now iterating at: 14:51:04 rms-change max change #iterations 0.1286373 20.77279 at 10iterations 1.3267466E-02 2.345154 at 20iterations 1.3686438E-03 0.2348022 at 30iterations 1.3990673E-04 2.2646904E-02 at 40iterations 1.4449502E-05 2.2621155E-03 at 50iterations finished qdiffx linear iterations at : 14:51:07 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.4449502E-05 2.2621155E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:51:07 3.356u 0.204s 0:03.96 89.6% 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 14:51:07 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 = 1866 !!! WARNING: GLU 107 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.961757 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): -17.89700 36.54400 ymin,ymax (A): -19.83700 28.78000 zmin,zma (A): -19.06800 31.19900 x,y,z range (A): 54.44100 48.61700 50.26700 scale (grids/A): 1.961757 object centre (A): 9.323500 4.471499 6.065501 number of atom coordinates read : 1866 total number of charged atoms : 1731 net assigned charge : 1.500004 assigned positive charge : 276.1492 centred at (gu) : 86.40340 87.02970 91.64765 assigned negative charge : -274.6493 centred at (gu) : 86.45634 87.67725 91.72535 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18910 grid for indexing accessible points = 1.400000 m= 21676 mr = 38994 m= 3305 mr = 15651 m= 177 mr = 1932 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 757 time to turn everything in is 0.3100000 number of dielectric boundary points 28786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 13641 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) : 0.6539189 object centre at (A) : 9.323500 4.471499 6.065501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2238283E-02 -1.1070469E-02 midg,1,midg; midg,igrid,midg 1.2461451E-02 -3.7996836E-03 1,midg,midg; igrid,midg,midg -1.5095516E-02 -1.7636864E-02 gauss-seidel spectral radius is 0.9986461 estimated iterations to convergence 215 setup time was (sec) 0.5300000 now iterating at: 14:51:08 rms-change max change #iterations 3.709754 164.2616 at 10iterations 1.740075 75.68016 at 20iterations 0.8180133 29.61047 at 30iterations 0.3840838 14.81006 at 40iterations 0.1799717 6.457422 at 50iterations 8.4407263E-02 3.346844 at 60iterations 3.9566796E-02 1.500385 at 70iterations 1.8561689E-02 0.6428285 at 80iterations 8.7031685E-03 0.3102188 at 90iterations 4.0812595E-03 0.1395073 at 100iterations 1.9110453E-03 6.4156532E-02 at 110iterations 8.9539407E-04 3.1878710E-02 at 120iterations finished qdiffx linear iterations at : 14:51:15 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 8.9539407E-04 3.1878710E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 14:51:15 7.815u 0.189s 0:08.34 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 14:51:16 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 = 1866 !!! WARNING: GLU 107 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.942635 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): -17.89700 36.54400 ymin,ymax (A): -19.83700 28.78000 zmin,zma (A): -19.06800 31.19900 x,y,z range (A): 54.44100 48.61700 50.26700 scale (grids/A): 2.942635 object centre (A): 9.323500 4.471499 6.065501 number of atom coordinates read : 1866 total number of charged atoms : 1731 net assigned charge : 1.500004 assigned positive charge : 276.1492 centred at (gu) : 84.60514 85.54458 92.47153 assigned negative charge : -274.6493 centred at (gu) : 84.68459 86.51584 92.58816 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 138489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18910 grid for indexing accessible points = 1.400000 m= 69498 mr = 94615 m= 25119 mr = 55743 m= 5714 mr = 19801 m= 721 mr = 4148 m= 47 mr = 409 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 2553 time to turn everything in is 0.7900000 number of dielectric boundary points 64850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 13848 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) : 1.961757 object centre at (A) : 9.323500 4.471499 6.065501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4701108E-02 -0.1840696 midg,1,midg; midg,igrid,midg -5.9916899E-02 -9.9917194E-03 1,midg,midg; igrid,midg,midg -0.3099383 -0.2084562 gauss-seidel spectral radius is 0.9992774 estimated iterations to convergence 294 setup time was (sec) 1.020000 now iterating at: 14:51:17 rms-change max change #iterations 8.852209 525.3710 at 10iterations 5.205832 171.3027 at 20iterations 3.040039 74.37219 at 30iterations 1.774448 43.17808 at 40iterations 1.030516 26.44909 at 50iterations 0.5989427 13.95442 at 60iterations 0.3477241 7.302352 at 70iterations 0.2010329 4.399781 at 80iterations 0.1162688 2.451920 at 90iterations 6.7320794E-02 1.678944 at 100iterations 3.8907982E-02 0.8109436 at 110iterations 2.2481892E-02 0.4576335 at 120iterations 1.2992949E-02 0.2445583 at 130iterations 7.5130071E-03 0.1550140 at 140iterations 4.3334528E-03 8.4426880E-02 at 150iterations 2.4987345E-03 4.9033642E-02 at 160iterations 1.4441373E-03 2.7880669E-02 at 170iterations 8.3485409E-04 1.6124725E-02 at 180iterations finished qdiffx linear iterations at : 14:51:28 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 8.3485409E-04 1.6124725E-02 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.35000 DelPhi exited at 14:51:28 12.349u 0.213s 0:12.82 97.8% 0+0k 0+0io 0pf+0w