Wed Dec 28 11:05:37 PST 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 Wed Dec 28 2011 at 11:05:37 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 0.6109071 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): -9.039000 49.23500 ymin,ymax (A): 8.652000 47.48300 zmin,zma (A): -3.712000 38.68000 x,y,z range (A): 58.27400 38.83100 42.39200 scale (grids/A): 0.6109071 object centre (A): 20.09800 28.06750 17.48400 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000005 assigned positive charge : 291.8040 centred at (gu) : 90.06733 89.84051 90.46593 assigned negative charge : -287.8043 centred at (gu) : 90.04638 89.74410 90.59264 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 4967 nv = 96 ne = 84 npr = 40186 no. pairs analyzed = 40186 no. exposed pairs = 2447 no. arc points = 17301 no. surface atoms = 828 nbur = 1140 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 203 mr = 2721 m= 0 mr = 15 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1746 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 5998 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4701369E-09 -2.6661113E-09 midg,1,midg; midg,igrid,midg -1.2603448E-09 5.8520593E-09 1,midg,midg; igrid,midg,midg 1.6505777E-09 3.3030971E-09 gauss-seidel spectral radius is 0.9860737 estimated iterations to convergence 69 setup time was (sec) 0.6100000 now iterating at: 11:05:38 rms-change max change #iterations 0.1065059 16.84951 at 10iterations 9.2925038E-03 1.390755 at 20iterations 8.1942719E-04 0.1401358 at 30iterations 7.2178533E-05 1.1938095E-02 at 40iterations 6.3016546E-06 9.7656250E-04 at 50iterations finished qdiffx linear iterations at : 11:05:41 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 6.3016546E-06 9.7656250E-04 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 11:05:42 3.974u 0.156s 0:04.52 91.1% 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 Wed Dec 28 2011 at 11:05:42 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.832721 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): -9.039000 49.23500 ymin,ymax (A): 8.652000 47.48300 zmin,zma (A): -3.712000 38.68000 x,y,z range (A): 58.27400 38.83100 42.39200 scale (grids/A): 1.832721 object centre (A): 20.09800 28.06750 17.48400 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000005 assigned positive charge : 291.8040 centred at (gu) : 90.20171 89.52161 91.39796 assigned negative charge : -287.8043 centred at (gu) : 90.13954 89.23241 91.77811 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 53965 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17301 grid for indexing accessible points = 1.400000 m= 18474 mr = 37148 m= 2272 mr = 13782 m= 59 mr = 1294 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1730 time to turn everything in is 0.5100000 number of dielectric boundary points 22538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 14410 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) : 0.6109071 object centre at (A) : 20.09800 28.06750 17.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0481565E-02 -3.6440000E-03 midg,1,midg; midg,igrid,midg 1.0194007E-04 6.2210979E-03 1,midg,midg; igrid,midg,midg 3.1397820E-02 3.7164543E-02 gauss-seidel spectral radius is 0.9984512 estimated iterations to convergence 202 setup time was (sec) 0.8400000 now iterating at: 11:05:43 rms-change max change #iterations 3.342966 169.1118 at 10iterations 1.492304 55.44105 at 20iterations 0.6649964 25.44960 at 30iterations 0.2963943 11.38866 at 40iterations 0.1323393 5.122253 at 50iterations 5.8797467E-02 2.146245 at 60iterations 2.6199361E-02 0.9543471 at 70iterations 1.1642827E-02 0.4832798 at 80iterations 5.2161841E-03 0.1968174 at 90iterations 2.3177890E-03 8.1821442E-02 at 100iterations 1.0356436E-03 3.6659718E-02 at 110iterations 4.6212410E-04 1.6538620E-02 at 120iterations finished qdiffx linear iterations at : 11:05:51 total time elapsed so far: 8.500000 # loops : 120 mean,max change (kT/e) : 4.6212410E-04 1.6538620E-02 energy calculations done at 8.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.730000 DelPhi exited at 11:05:51 8.729u 0.186s 0:09.22 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 Wed Dec 28 2011 at 11:05:51 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 2.749082 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): -9.039000 49.23500 ymin,ymax (A): 8.652000 47.48300 zmin,zma (A): -3.712000 38.68000 x,y,z range (A): 58.27400 38.83100 42.39200 scale (grids/A): 2.749082 object centre (A): 20.09800 28.06750 17.48400 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000005 assigned positive charge : 291.8040 centred at (gu) : 90.30262 89.28230 92.09691 assigned negative charge : -287.8043 centred at (gu) : 90.20927 88.84872 92.66714 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 124726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17301 grid for indexing accessible points = 1.400000 m= 61639 mr = 89734 m= 20288 mr = 50846 m= 3833 mr = 16439 m= 296 mr = 2830 m= 4 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 5970 time to turn everything in is 1.190000 number of dielectric boundary points 50812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 14688 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) : 1.832721 object centre at (A) : 20.09800 28.06750 17.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5814103E-02 -2.2503347E-03 midg,1,midg; midg,igrid,midg 2.5920177E-02 4.7557134E-02 1,midg,midg; igrid,midg,midg 0.4302009 0.4571745 gauss-seidel spectral radius is 0.9991906 estimated iterations to convergence 278 setup time was (sec) 1.550000 now iterating at: 11:05:53 rms-change max change #iterations 7.961511 341.0499 at 10iterations 4.489390 137.4195 at 20iterations 2.518133 57.48231 at 30iterations 1.410416 32.59633 at 40iterations 0.7913899 16.28473 at 50iterations 0.4417917 9.464989 at 60iterations 0.2465191 6.499456 at 70iterations 0.1378728 3.327179 at 80iterations 7.6890364E-02 1.714119 at 90iterations 4.2937975E-02 0.8888550 at 100iterations 2.3998542E-02 0.5122643 at 110iterations 1.3420264E-02 0.2886095 at 120iterations 7.4997265E-03 0.1960831 at 130iterations 4.1979132E-03 9.2712402E-02 at 140iterations 2.3376474E-03 4.5419693E-02 at 150iterations 1.3050709E-03 2.5978684E-02 at 160iterations 7.2877447E-04 1.5525341E-02 at 170iterations 4.0731818E-04 8.9750290E-03 at 180iterations finished qdiffx linear iterations at : 11:06:05 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 4.0731818E-04 8.9750290E-03 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 11:06:05 13.469u 0.196s 0:13.99 97.5% 0+0k 0+0io 0pf+0w