Mon Oct 10 23:39:42 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 23:39:43 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 !!! 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5679914 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): 10.97000 64.60900 ymin,ymax (A): -3.629000 59.04800 zmin,zma (A): 10.87700 54.09300 x,y,z range (A): 53.63900 62.67700 43.21600 scale (grids/A): 0.5679914 object centre (A): 37.78950 27.70950 32.48500 number of atom coordinates read : 2623 total number of charged atoms : 2479 net assigned charge : 8.906017 assigned positive charge : 396.9509 centred at (gu) : 88.93333 91.42319 89.76559 assigned negative charge : -388.0454 centred at (gu) : 88.93457 91.28422 89.89152 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5485 nv = 96 ne = 84 npr = 52598 no. pairs analyzed = 52598 no. exposed pairs = 3176 no. arc points = 22253 no. surface atoms = 1072 nbur = 1551 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 251 mr = 2986 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3800000 number of dielectric boundary points 2735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2242 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7028 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9805274E-09 -3.7096576E-10 midg,1,midg; midg,igrid,midg -3.8793108E-10 4.1931094E-09 1,midg,midg; igrid,midg,midg 1.6041426E-09 9.5525476E-10 gauss-seidel spectral radius is 0.9839743 estimated iterations to convergence 65 setup time was (sec) 0.6600000 now iterating at: 23:39:44 rms-change max change #iterations 8.6196534E-02 15.81605 at 10iterations 7.1879453E-03 1.066971 at 20iterations 8.9972670E-04 0.2201233 at 30iterations 1.9881839E-04 5.3241730E-02 at 40iterations 4.9287679E-05 1.3267517E-02 at 50iterations finished qdiffx linear iterations at : 23:39:47 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 4.9287679E-05 1.3267517E-02 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 23:39:47 4.030u 0.164s 0:04.52 92.6% 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 Mon Oct 10 2011 at 23:39:47 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.703974 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): 10.97000 64.60900 ymin,ymax (A): -3.629000 59.04800 zmin,zma (A): 10.87700 54.09300 x,y,z range (A): 53.63900 62.67700 43.21600 scale (grids/A): 1.703974 object centre (A): 37.78950 27.70950 32.48500 number of atom coordinates read : 2623 total number of charged atoms : 2479 net assigned charge : 8.906017 assigned positive charge : 396.9509 centred at (gu) : 86.79956 94.26882 89.29593 assigned negative charge : -388.0454 centred at (gu) : 86.80363 93.85241 89.67446 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 60431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22253 grid for indexing accessible points = 1.400000 m= 19752 mr = 41793 m= 2290 mr = 14061 m= 75 mr = 1205 m= 0 mr = 1 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 466 time to turn everything in is 0.5700000 number of dielectric boundary points 25488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 264 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19210 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) : 0.5679914 object centre at (A) : 37.78950 27.70950 32.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9041834E-02 1.7534200E-03 midg,1,midg; midg,igrid,midg 6.9144422E-05 -7.7404287E-03 1,midg,midg; igrid,midg,midg 2.2832109E-03 9.3112560E-03 gauss-seidel spectral radius is 0.9982956 estimated iterations to convergence 192 setup time was (sec) 0.9200000 now iterating at: 23:39:48 rms-change max change #iterations 3.363270 146.6552 at 10iterations 1.430540 58.62125 at 20iterations 0.6166959 24.32620 at 30iterations 0.2638830 9.953388 at 40iterations 0.1138928 4.176180 at 50iterations 4.8573315E-02 1.674798 at 60iterations 2.0953147E-02 0.7716141 at 70iterations 9.1025783E-03 0.3480225 at 80iterations 4.0317969E-03 0.1522255 at 90iterations 1.8360114E-03 7.8987122E-02 at 100iterations 8.7886525E-04 3.6945343E-02 at 110iterations 4.4367308E-04 2.0656586E-02 at 120iterations finished qdiffx linear iterations at : 23:39:56 total time elapsed so far: 8.480000 # loops : 120 mean,max change (kT/e) : 4.4367308E-04 2.0656586E-02 energy calculations done at 8.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.710000 DelPhi exited at 23:39:57 8.715u 0.181s 0:09.42 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 Mon Oct 10 2011 at 23:39:57 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.555961 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): 10.97000 64.60900 ymin,ymax (A): -3.629000 59.04800 zmin,zma (A): 10.87700 54.09300 x,y,z range (A): 53.63900 62.67700 43.21600 scale (grids/A): 2.555961 object centre (A): 37.78950 27.70950 32.48500 number of atom coordinates read : 2623 total number of charged atoms : 2479 net assigned charge : 8.906017 assigned positive charge : 396.9509 centred at (gu) : 85.19909 96.40317 88.94377 assigned negative charge : -388.0454 centred at (gu) : 85.20541 95.77851 89.51155 start vw surface at 0.1900000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 140390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22253 grid for indexing accessible points = 1.400000 m= 66953 mr = 101914 m= 20720 mr = 54082 m= 3800 mr = 16048 m= 275 mr = 2550 m= 13 mr = 91 m= 0 mr = 3 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 1760 time to turn everything in is 1.350000 number of dielectric boundary points 57463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 19828 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) : 1.703974 object centre at (A) : 37.78950 27.70950 32.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2477889 3.9467096E-02 midg,1,midg; midg,igrid,midg -9.8560795E-02 -0.4676613 1,midg,midg; igrid,midg,midg -1.5589602E-02 9.2329293E-02 gauss-seidel spectral radius is 0.9991564 estimated iterations to convergence 272 setup time was (sec) 1.680000 now iterating at: 23:39:59 rms-change max change #iterations 8.427820 269.0446 at 10iterations 4.700469 108.4215 at 20iterations 2.627000 62.91509 at 30iterations 1.458638 32.91886 at 40iterations 0.8132912 18.00224 at 50iterations 0.4504350 9.283784 at 60iterations 0.2494680 5.261180 at 70iterations 0.1384456 3.008545 at 80iterations 7.6609686E-02 1.752064 at 90iterations 4.2527687E-02 0.8951329 at 100iterations 2.3530794E-02 0.4897003 at 110iterations 1.3118108E-02 0.2842891 at 120iterations 7.3116194E-03 0.1456490 at 130iterations 4.0969709E-03 0.1090851 at 140iterations 2.3287928E-03 4.9217224E-02 at 150iterations 1.3534167E-03 3.1719208E-02 at 160iterations 8.1112492E-04 2.2518158E-02 at 170iterations 5.0604821E-04 1.4728546E-02 at 180iterations finished qdiffx linear iterations at : 23:40:10 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 5.0604821E-04 1.4728546E-02 energy calculations done at 13.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.68000 DelPhi exited at 23:40:11 13.686u 0.216s 0:14.42 96.3% 0+0k 0+0io 0pf+0w