Sun Oct 9 07:49:46 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 07:49:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NAP 207 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6994381 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): -16.35900 30.77000 ymin,ymax (A): -20.29200 30.60600 zmin,zma (A): -4.563000 34.36000 x,y,z range (A): 47.12900 50.89800 38.92300 scale (grids/A): 0.6994381 object centre (A): 7.205501 5.157000 14.89850 number of atom coordinates read : 2215 total number of charged atoms : 2078 net assigned charge : 6.000018 assigned positive charge : 332.2886 centred at (gu) : 89.92002 90.68498 91.04398 assigned negative charge : -326.2889 centred at (gu) : 89.78173 90.78236 91.18867 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7403 nv = 96 ne = 84 npr = 45766 no. pairs analyzed = 45766 no. exposed pairs = 2717 no. arc points = 19460 no. surface atoms = 911 nbur = 1304 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 481 mr = 4155 m= 6 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 99 time to turn everything in is 0.2900000 number of dielectric boundary points 3659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1859 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5138048E-08 -2.5741095E-08 midg,1,midg; midg,igrid,midg 7.3967769E-08 2.9374159E-10 1,midg,midg; igrid,midg,midg -1.7778431E-08 1.0016608E-07 gauss-seidel spectral radius is 0.9893655 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 07:49:47 rms-change max change #iterations 0.1973466 27.44793 at 10iterations 2.3710189E-02 3.533112 at 20iterations 2.8678020E-03 0.4325609 at 30iterations 3.4381959E-04 4.2193413E-02 at 40iterations 4.1391679E-05 5.6650639E-03 at 50iterations finished qdiffx linear iterations at : 07:49:49 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 4.1391679E-05 5.6650639E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 07:49:50 3.498u 0.222s 0:03.99 92.9% 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 07:49:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NAP 207 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.098314 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): -16.35900 30.77000 ymin,ymax (A): -20.29200 30.60600 zmin,zma (A): -4.563000 34.36000 x,y,z range (A): 47.12900 50.89800 38.92300 scale (grids/A): 2.098314 object centre (A): 7.205501 5.157000 14.89850 number of atom coordinates read : 2215 total number of charged atoms : 2078 net assigned charge : 6.000018 assigned positive charge : 332.2886 centred at (gu) : 89.75982 92.05492 93.13162 assigned negative charge : -326.2889 centred at (gu) : 89.34518 92.34709 93.56561 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19460 grid for indexing accessible points = 1.400000 m= 30865 mr = 53838 m= 6202 mr = 23592 m= 668 mr = 4207 m= 24 mr = 356 m= 0 mr = 6 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1798 time to turn everything in is 0.5900000 number of dielectric boundary points 33387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 16499 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) : 0.6994381 object centre at (A) : 7.205501 5.157000 14.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1114114E-02 2.7576711E-03 midg,1,midg; midg,igrid,midg 3.0993732E-02 2.4659829E-02 1,midg,midg; igrid,midg,midg -1.5800865E-02 4.2379975E-02 gauss-seidel spectral radius is 0.9988267 estimated iterations to convergence 231 setup time was (sec) 0.9000000 now iterating at: 07:49:51 rms-change max change #iterations 4.688789 212.4027 at 10iterations 2.304132 81.57283 at 20iterations 1.141399 35.46824 at 30iterations 0.5668547 18.37520 at 40iterations 0.2804660 8.595791 at 50iterations 0.1389154 3.973312 at 60iterations 6.8636991E-02 2.235293 at 70iterations 3.4012441E-02 1.091573 at 80iterations 1.6844139E-02 0.4781771 at 90iterations 8.3807576E-03 0.2448993 at 100iterations 4.1345069E-03 0.1440452 at 110iterations 2.0425222E-03 6.3300133E-02 at 120iterations finished qdiffx linear iterations at : 07:49:58 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.0425222E-03 6.3300133E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 07:49:58 7.968u 0.263s 0:08.50 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 Sun Oct 9 2011 at 07:49:58 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NAP 207 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.147471 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): -16.35900 30.77000 ymin,ymax (A): -20.29200 30.60600 zmin,zma (A): -4.563000 34.36000 x,y,z range (A): 47.12900 50.89800 38.92300 scale (grids/A): 3.147471 object centre (A): 7.205501 5.157000 14.89850 number of atom coordinates read : 2215 total number of charged atoms : 2078 net assigned charge : 6.000018 assigned positive charge : 332.2886 centred at (gu) : 89.63985 93.08235 94.69739 assigned negative charge : -326.2889 centred at (gu) : 89.01778 93.52065 95.34842 start vw surface at 0.1400000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 178815 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19460 grid for indexing accessible points = 1.400000 m= 95526 mr = 129693 m= 39851 mr = 79568 m= 11793 mr = 33102 m= 2565 mr = 9197 m= 347 mr = 1834 m= 25 mr = 251 m= 0 mr = 9 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 6098 time to turn everything in is 1.790000 number of dielectric boundary points 75268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 16624 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) : 2.098314 object centre at (A) : 7.205501 5.157000 14.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5981370 1.5292867E-03 midg,1,midg; midg,igrid,midg 0.1477579 0.3047189 1,midg,midg; igrid,midg,midg -8.3468787E-02 0.3055065 gauss-seidel spectral radius is 0.9992909 estimated iterations to convergence 296 setup time was (sec) 2.120000 now iterating at: 07:50:01 rms-change max change #iterations 10.31432 411.3749 at 10iterations 5.988545 131.6298 at 20iterations 3.480240 63.30769 at 30iterations 2.024354 35.24704 at 40iterations 1.173331 21.14518 at 50iterations 0.6825585 11.34764 at 60iterations 0.3962663 6.977611 at 70iterations 0.2299531 3.820686 at 80iterations 0.1333020 2.236714 at 90iterations 7.7327885E-02 1.316890 at 100iterations 4.4935506E-02 0.7786980 at 110iterations 2.6058439E-02 0.4415212 at 120iterations 1.5157757E-02 0.2527828 at 130iterations 8.7760780E-03 0.1537485 at 140iterations 5.0960239E-03 8.8470459E-02 at 150iterations 2.9647304E-03 4.8942566E-02 at 160iterations 1.7174345E-03 2.8500557E-02 at 170iterations 9.9971972E-04 1.6487122E-02 at 180iterations finished qdiffx linear iterations at : 07:50:12 total time elapsed so far: 13.30000 # loops : 180 mean,max change (kT/e) : 9.9971972E-04 1.6487122E-02 energy calculations done at 13.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 07:50:12 13.484u 0.281s 0:14.05 97.9% 0+0k 0+0io 0pf+0w