Tue Oct 11 07:58:07 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 Tue Oct 11 2011 at 07:58:07 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 = 2314 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: 0.6696386 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): -58.19000 -5.027000 ymin,ymax (A): 65.86200 108.1660 zmin,zma (A): -24.96600 19.45300 x,y,z range (A): 53.16300 42.30400 44.41900 scale (grids/A): 0.6696386 object centre (A): -31.60850 87.01400 -2.756500 number of atom coordinates read : 2314 total number of charged atoms : 2190 net assigned charge : 4.500008 assigned positive charge : 347.1555 centred at (gu) : 91.55147 90.33530 90.65116 assigned negative charge : -342.6558 centred at (gu) : 91.68094 90.50774 90.57233 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6896 nv = 96 ne = 84 npr = 47140 no. pairs analyzed = 47140 no. exposed pairs = 2795 no. arc points = 19975 no. surface atoms = 943 nbur = 1371 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 363 mr = 3841 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 126 time to turn everything in is 0.1700000 number of dielectric boundary points 3375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1870 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8113 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9230899E-09 3.7369315E-08 midg,1,midg; midg,igrid,midg 4.9417419E-08 -2.5458057E-08 1,midg,midg; igrid,midg,midg 3.1863276E-08 -1.9578433E-08 gauss-seidel spectral radius is 0.9884110 estimated iterations to convergence 76 setup time was (sec) 0.3700000 now iterating at: 07:58:07 rms-change max change #iterations 0.1645592 26.81749 at 10iterations 1.8064808E-02 2.291820 at 20iterations 1.9965461E-03 0.2929840 at 30iterations 2.1546790E-04 3.2905340E-02 at 40iterations 2.3422535E-05 3.2958984E-03 at 50iterations finished qdiffx linear iterations at : 07:58:10 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.3422535E-05 3.2958984E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 07:58:11 3.320u 0.171s 0:03.90 89.4% 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 Tue Oct 11 2011 at 07:58:11 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 = 2314 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: 2.008916 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): -58.19000 -5.027000 ymin,ymax (A): 65.86200 108.1660 zmin,zma (A): -24.96600 19.45300 x,y,z range (A): 53.16300 42.30400 44.41900 scale (grids/A): 2.008916 object centre (A): -31.60850 87.01400 -2.756500 number of atom coordinates read : 2314 total number of charged atoms : 2190 net assigned charge : 4.500008 assigned positive charge : 347.1555 centred at (gu) : 94.65407 91.00547 91.95310 assigned negative charge : -342.6558 centred at (gu) : 95.04281 91.52304 91.71697 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 74007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19975 grid for indexing accessible points = 1.400000 m= 27598 mr = 51627 m= 4656 mr = 20656 m= 324 mr = 3047 m= 7 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1312 time to turn everything in is 0.3800000 number of dielectric boundary points 31140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17327 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) : 0.6696386 object centre at (A) : -31.60850 87.01400 -2.756500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4202876E-02 3.0912807E-02 midg,1,midg; midg,igrid,midg 2.4786284E-02 -2.4773693E-02 1,midg,midg; igrid,midg,midg 5.2731253E-02 2.9292608E-02 gauss-seidel spectral radius is 0.9987370 estimated iterations to convergence 223 setup time was (sec) 0.6000000 now iterating at: 07:58:11 rms-change max change #iterations 4.363529 207.1198 at 10iterations 2.097340 84.35106 at 20iterations 1.010737 35.66851 at 30iterations 0.4875364 15.10137 at 40iterations 0.2360586 7.369583 at 50iterations 0.1135677 4.008072 at 60iterations 5.4778650E-02 1.764629 at 70iterations 2.6460296E-02 0.8629103 at 80iterations 1.2771365E-02 0.4003752 at 90iterations 6.1455113E-03 0.2007403 at 100iterations 2.9714743E-03 9.7766876E-02 at 110iterations 1.4335965E-03 4.3899536E-02 at 120iterations finished qdiffx linear iterations at : 07:58:18 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.4335965E-03 4.3899536E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 07:58:19 7.823u 0.194s 0:08.49 94.3% 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 Tue Oct 11 2011 at 07:58:19 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 = 2314 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: 3.013374 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): -58.19000 -5.027000 ymin,ymax (A): 65.86200 108.1660 zmin,zma (A): -24.96600 19.45300 x,y,z range (A): 53.16300 42.30400 44.41900 scale (grids/A): 3.013374 object centre (A): -31.60850 87.01400 -2.756500 number of atom coordinates read : 2314 total number of charged atoms : 2190 net assigned charge : 4.500008 assigned positive charge : 347.1555 centred at (gu) : 96.98098 91.50819 92.92957 assigned negative charge : -342.6558 centred at (gu) : 97.56414 92.28454 92.57534 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 170615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19975 grid for indexing accessible points = 1.400000 m= 88176 mr = 124447 m= 33054 mr = 72860 m= 8599 mr = 26884 m= 1376 mr = 6624 m= 104 mr = 916 m= 7 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 4561 time to turn everything in is 0.9400000 number of dielectric boundary points 70134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 17518 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) : 2.008916 object centre at (A) : -31.60850 87.01400 -2.756500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2290726 0.3201168 midg,1,midg; midg,igrid,midg 0.1486650 -0.2946501 1,midg,midg; igrid,midg,midg 0.6030821 0.3074621 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 1.170000 now iterating at: 07:58:21 rms-change max change #iterations 10.04310 550.1571 at 10iterations 5.869075 151.2288 at 20iterations 3.426616 69.10783 at 30iterations 1.998066 40.19208 at 40iterations 1.160688 22.60989 at 50iterations 0.6749833 12.73943 at 60iterations 0.3919784 7.446899 at 70iterations 0.2273027 4.057404 at 80iterations 0.1317455 2.608837 at 90iterations 7.6066740E-02 1.385658 at 100iterations 4.3986179E-02 0.8284912 at 110iterations 2.5534905E-02 0.4568157 at 120iterations 1.4755582E-02 0.2567043 at 130iterations 8.5451650E-03 0.1557846 at 140iterations 4.9313679E-03 8.7558746E-02 at 150iterations 2.8534615E-03 5.1108360E-02 at 160iterations 1.6537141E-03 2.8941154E-02 at 170iterations 9.5612009E-04 1.7468452E-02 at 180iterations finished qdiffx linear iterations at : 07:58:32 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 9.5612009E-04 1.7468452E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 07:58:32 12.369u 0.211s 0:12.88 97.5% 0+0k 0+0io 0pf+0w