Tue Oct 11 07:35:49 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 Tue Oct 11 2011 at 07:35:49 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3315 !!! WARNING: UMP 564 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6059161 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): 69.55700 128.3110 ymin,ymax (A): -44.18300 6.729000 zmin,zma (A): 6.689000 60.68400 x,y,z range (A): 58.75401 50.91200 53.99500 scale (grids/A): 0.6059161 object centre (A): 98.93401 -18.72700 33.68650 number of atom coordinates read : 3315 total number of charged atoms : 3173 net assigned charge : 5.900031 assigned positive charge : 501.7096 centred at (gu) : 89.41140 90.56320 89.22910 assigned negative charge : -495.8111 centred at (gu) : 89.25819 90.58588 89.17451 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8147 nv = 96 ne = 84 npr = 67098 no. pairs analyzed = 67098 no. exposed pairs = 3966 no. arc points = 27152 no. surface atoms = 1357 nbur = 1958 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 4667 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2400000 number of dielectric boundary points 3855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2849 ## 313 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 10110 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2203320E-11 5.2091260E-09 midg,1,midg; midg,igrid,midg 3.9025116E-09 2.1227358E-09 1,midg,midg; igrid,midg,midg -6.3816983E-09 1.0125141E-08 gauss-seidel spectral radius is 0.9859597 estimated iterations to convergence 69 setup time was (sec) 0.4300000 now iterating at: 07:35:49 rms-change max change #iterations 0.1286505 21.25133 at 10iterations 1.1750975E-02 1.644264 at 20iterations 1.7524782E-03 0.2415791 at 30iterations 6.6635950E-04 0.1000929 at 40iterations 3.0344506E-04 4.6875000E-02 at 50iterations finished qdiffx linear iterations at : 07:35:52 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 3.0344506E-04 4.6875000E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 07:35:53 3.449u 0.177s 0:03.98 90.7% 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 Tue Oct 11 2011 at 07:35:53 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3315 !!! WARNING: UMP 564 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.817748 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): 69.55700 128.3110 ymin,ymax (A): -44.18300 6.729000 zmin,zma (A): 6.689000 60.68400 x,y,z range (A): 58.75401 50.91200 53.99500 scale (grids/A): 1.817748 object centre (A): 98.93401 -18.72700 33.68650 number of atom coordinates read : 3315 total number of charged atoms : 3173 net assigned charge : 5.900031 assigned positive charge : 501.7096 centred at (gu) : 88.23357 91.68888 87.68678 assigned negative charge : -495.8111 centred at (gu) : 87.77447 91.75726 87.52329 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 88439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27152 grid for indexing accessible points = 1.400000 m= 32140 mr = 62781 m= 4655 mr = 24102 m= 188 mr = 2954 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 35525 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 24804 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) : 0.6059161 object centre at (A) : 98.93401 -18.72700 33.68650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4243115E-02 5.3275976E-02 midg,1,midg; midg,igrid,midg -5.1945248E-03 -1.0277085E-02 1,midg,midg; igrid,midg,midg -2.1203486E-02 2.1285418E-02 gauss-seidel spectral radius is 0.9985774 estimated iterations to convergence 210 setup time was (sec) 0.6500000 now iterating at: 07:35:54 rms-change max change #iterations 4.469459 165.2115 at 10iterations 2.054671 64.64875 at 20iterations 0.9482788 29.98178 at 30iterations 0.4366975 13.67118 at 40iterations 0.2021328 6.055017 at 50iterations 9.3411721E-02 2.832565 at 60iterations 4.3332137E-02 1.279396 at 70iterations 2.0113889E-02 0.6430626 at 80iterations 9.5091956E-03 0.2813249 at 90iterations 4.6506720E-03 0.1303797 at 100iterations 2.4099434E-03 8.1501007E-02 at 110iterations 1.3881307E-03 5.0142288E-02 at 120iterations finished qdiffx linear iterations at : 07:36:01 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.3881307E-03 5.0142288E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 07:36:01 7.963u 0.202s 0:08.45 96.5% 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 07:36:01 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3315 !!! WARNING: UMP 564 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.726623 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): 69.55700 128.3110 ymin,ymax (A): -44.18300 6.729000 zmin,zma (A): 6.689000 60.68400 x,y,z range (A): 58.75401 50.91200 53.99500 scale (grids/A): 2.726623 object centre (A): 98.93401 -18.72700 33.68650 number of atom coordinates read : 3315 total number of charged atoms : 3173 net assigned charge : 5.900031 assigned positive charge : 501.7096 centred at (gu) : 87.35018 92.53319 86.52987 assigned negative charge : -495.8111 centred at (gu) : 86.66163 92.63589 86.28479 start vw surface at 0.1100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 204650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27152 grid for indexing accessible points = 1.400000 m= 105091 mr = 151766 m= 37208 mr = 87058 m= 8156 mr = 30351 m= 884 mr = 6190 m= 41 mr = 587 m= 0 mr = 10 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.120000 number of dielectric boundary points 80068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 25380 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) : 1.817748 object centre at (A) : 98.93401 -18.72700 33.68650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2960476 1.007625 midg,1,midg; midg,igrid,midg -0.1246759 -0.2334785 1,midg,midg; igrid,midg,midg -8.8031851E-02 0.2667188 gauss-seidel spectral radius is 0.9992547 estimated iterations to convergence 289 setup time was (sec) 1.360000 now iterating at: 07:36:03 rms-change max change #iterations 10.55796 304.1262 at 10iterations 6.161826 136.6800 at 20iterations 3.564599 63.64998 at 30iterations 2.068182 36.60374 at 40iterations 1.190861 23.24939 at 50iterations 0.6867617 11.70009 at 60iterations 0.3949892 7.611454 at 70iterations 0.2270147 3.850613 at 80iterations 0.1308376 2.544857 at 90iterations 7.5114235E-02 1.257759 at 100iterations 4.3254670E-02 0.7468586 at 110iterations 2.4948709E-02 0.4308600 at 120iterations 1.4440838E-02 0.2609673 at 130iterations 8.4469691E-03 0.1566010 at 140iterations 5.0480384E-03 9.0828419E-02 at 150iterations 3.1352097E-03 6.3111305E-02 at 160iterations 2.0718761E-03 4.1870117E-02 at 170iterations 1.4736132E-03 3.1146049E-02 at 180iterations finished qdiffx linear iterations at : 07:36:14 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 1.4736132E-03 3.1146049E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 07:36:15 13.061u 0.199s 0:13.87 95.5% 0+0k 0+0io 0pf+0w