Mon Oct 10 23:53:12 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 23:53:12 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2662 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 0.6314072 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): 18.02300 74.34600 ymin,ymax (A): -11.51200 44.87000 zmin,zma (A): -7.709000 35.10800 x,y,z range (A): 56.32300 56.38200 42.81700 scale (grids/A): 0.6314072 object centre (A): 46.18450 16.67900 13.69950 number of atom coordinates read : 2662 total number of charged atoms : 2514 net assigned charge : 2.406013 assigned positive charge : 401.8788 centred at (gu) : 88.55669 89.38384 89.82314 assigned negative charge : -399.4734 centred at (gu) : 88.78205 89.53354 90.02068 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7035 nv = 96 ne = 84 npr = 54683 no. pairs analyzed = 54683 no. exposed pairs = 3104 no. arc points = 21802 no. surface atoms = 1055 nbur = 1607 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 4044 m= 0 mr = 64 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.3900000 number of dielectric boundary points 3291 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2105 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8565 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1395962E-08 -1.6148373E-08 midg,1,midg; midg,igrid,midg 1.8578305E-08 -1.0542583E-08 1,midg,midg; igrid,midg,midg 3.1783490E-08 -1.4214830E-08 gauss-seidel spectral radius is 0.9870076 estimated iterations to convergence 72 setup time was (sec) 0.7300000 now iterating at: 23:53:14 rms-change max change #iterations 0.1397795 19.91637 at 10iterations 1.4143355E-02 2.056267 at 20iterations 1.8222516E-03 0.3221283 at 30iterations 4.3774204E-04 9.3734741E-02 at 40iterations 1.2736647E-04 2.9216766E-02 at 50iterations finished qdiffx linear iterations at : 23:53:17 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 1.2736647E-04 2.9216766E-02 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 23:53:18 4.548u 0.392s 0:05.29 93.1% 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 23:53:18 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2662 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 1.894222 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): 18.02300 74.34600 ymin,ymax (A): -11.51200 44.87000 zmin,zma (A): -7.709000 35.10800 x,y,z range (A): 56.32300 56.38200 42.81700 scale (grids/A): 1.894222 object centre (A): 46.18450 16.67900 13.69950 number of atom coordinates read : 2662 total number of charged atoms : 2514 net assigned charge : 2.406013 assigned positive charge : 401.8788 centred at (gu) : 85.66938 88.15096 89.46874 assigned negative charge : -399.4734 centred at (gu) : 86.34576 88.60023 90.06168 start vw surface at 0.1400000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 76866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21802 grid for indexing accessible points = 1.400000 m= 27127 mr = 54647 m= 4104 mr = 20421 m= 211 mr = 2679 m= 0 mr = 66 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1350 time to turn everything in is 0.7400000 number of dielectric boundary points 30495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 19796 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) : 0.6314072 object centre at (A) : 46.18450 16.67900 13.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7064482E-02 1.3832012E-03 midg,1,midg; midg,igrid,midg 4.8425615E-02 -2.9546905E-02 1,midg,midg; igrid,midg,midg -2.1816183E-02 -6.9561161E-02 gauss-seidel spectral radius is 0.9986198 estimated iterations to convergence 213 setup time was (sec) 1.080000 now iterating at: 23:53:19 rms-change max change #iterations 4.302440 200.9100 at 10iterations 2.000422 73.59734 at 20iterations 0.9333584 29.64635 at 30iterations 0.4344990 15.06131 at 40iterations 0.2040991 6.933922 at 50iterations 9.5034368E-02 3.010853 at 60iterations 4.4412185E-02 1.417059 at 70iterations 2.0959238E-02 0.6297989 at 80iterations 9.8868981E-03 0.3637161 at 90iterations 4.7586872E-03 0.1535354 at 100iterations 2.3582685E-03 8.8837624E-02 at 110iterations 1.2289258E-03 4.5532227E-02 at 120iterations finished qdiffx linear iterations at : 23:53:28 total time elapsed so far: 10.07000 # loops : 120 mean,max change (kT/e) : 1.2289258E-03 4.5532227E-02 energy calculations done at 10.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.28000 DelPhi exited at 23:53:29 10.289u 0.471s 0:11.11 96.7% 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 23:53:29 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2662 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 2.841332 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): 18.02300 74.34600 ymin,ymax (A): -11.51200 44.87000 zmin,zma (A): -7.709000 35.10800 x,y,z range (A): 56.32300 56.38200 42.81700 scale (grids/A): 2.841332 object centre (A): 46.18450 16.67900 13.69950 number of atom coordinates read : 2662 total number of charged atoms : 2514 net assigned charge : 2.406013 assigned positive charge : 401.8788 centred at (gu) : 83.50403 87.22630 89.20289 assigned negative charge : -399.4734 centred at (gu) : 84.51861 87.90034 90.09241 start vw surface at 0.1500000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 178124 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21802 grid for indexing accessible points = 1.400000 m= 89699 mr = 132513 m= 31503 mr = 74352 m= 7376 mr = 25688 m= 927 mr = 5676 m= 38 mr = 607 m= 0 mr = 19 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 4592 time to turn everything in is 2.020000 number of dielectric boundary points 68812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 20108 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) : 1.894222 object centre at (A) : 46.18450 16.67900 13.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3845843 5.6119971E-02 midg,1,midg; midg,igrid,midg 0.6717837 -0.5003809 1,midg,midg; igrid,midg,midg -0.2148553 -0.7754173 gauss-seidel spectral radius is 0.9992509 estimated iterations to convergence 288 setup time was (sec) 2.370000 now iterating at: 23:53:32 rms-change max change #iterations 10.01841 472.6947 at 10iterations 5.786762 113.4791 at 20iterations 3.325147 63.48931 at 30iterations 1.911510 34.59304 at 40iterations 1.096818 21.08406 at 50iterations 0.6272103 11.35115 at 60iterations 0.3598312 7.251602 at 70iterations 0.2064146 4.056492 at 80iterations 0.1182624 2.242020 at 90iterations 6.7727283E-02 1.197108 at 100iterations 3.8857009E-02 0.7160835 at 110iterations 2.2341551E-02 0.4409447 at 120iterations 1.2897259E-02 0.2480164 at 130iterations 7.4882940E-03 0.1385002 at 140iterations 4.4072755E-03 8.6135864E-02 at 150iterations 2.6491394E-03 6.1595917E-02 at 160iterations 1.6582191E-03 3.7139893E-02 at 170iterations 1.0930165E-03 2.5779724E-02 at 180iterations finished qdiffx linear iterations at : 23:53:47 total time elapsed so far: 17.34000 # loops : 180 mean,max change (kT/e) : 1.0930165E-03 2.5779724E-02 energy calculations done at 17.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.56000 DelPhi exited at 23:53:48 17.564u 0.473s 0:18.57 97.0% 0+0k 0+0io 0pf+0w