Tue Oct 11 00:49:04 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 00:49:04 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2714 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -0.2720 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: 0.5610275 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): -37.04100 26.41400 ymin,ymax (A): 32.59500 86.90000 zmin,zma (A): -7.287000 35.54500 x,y,z range (A): 63.45500 54.30500 42.83200 scale (grids/A): 0.5610275 object centre (A): -5.313500 59.74750 14.12900 number of atom coordinates read : 2714 total number of charged atoms : 2561 net assigned charge : 4.040014 assigned positive charge : 409.1027 centred at (gu) : 92.62012 90.41664 89.87885 assigned negative charge : -405.0633 centred at (gu) : 92.39365 90.31358 90.07464 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5510 nv = 96 ne = 84 npr = 55176 no. pairs analyzed = 55176 no. exposed pairs = 3200 no. arc points = 22594 no. surface atoms = 1081 nbur = 1633 mkacc time = 0.1600000 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 = 1.540000 m= 208 mr = 3006 m= 0 mr = 8 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 2704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2255 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7137 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4296536E-09 -1.6632851E-09 midg,1,midg; midg,igrid,midg -6.4256528E-10 1.5815315E-09 1,midg,midg; igrid,midg,midg -1.0796773E-09 5.0905640E-09 gauss-seidel spectral radius is 0.9835845 estimated iterations to convergence 64 setup time was (sec) 0.6300000 now iterating at: 00:49:05 rms-change max change #iterations 8.4455535E-02 15.95054 at 10iterations 6.9824932E-03 1.221275 at 20iterations 9.7996264E-04 0.2537270 at 30iterations 2.4152658E-04 6.6158295E-02 at 40iterations 6.3639156E-05 1.7520905E-02 at 50iterations finished qdiffx linear iterations at : 00:49:08 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 6.3639156E-05 1.7520905E-02 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 00:49:08 4.077u 0.251s 0:04.66 92.7% 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 00:49:09 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2714 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -0.2720 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: 1.683082 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): -37.04100 26.41400 ymin,ymax (A): 32.59500 86.90000 zmin,zma (A): -7.287000 35.54500 x,y,z range (A): 63.45500 54.30500 42.83200 scale (grids/A): 1.683082 object centre (A): -5.313500 59.74750 14.12900 number of atom coordinates read : 2714 total number of charged atoms : 2561 net assigned charge : 4.040014 assigned positive charge : 409.1027 centred at (gu) : 97.85989 91.24923 89.63581 assigned negative charge : -405.0633 centred at (gu) : 97.18066 90.94030 90.22379 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 61472 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22594 grid for indexing accessible points = 1.400000 m= 19228 mr = 42914 m= 2113 mr = 13727 m= 69 mr = 1132 m= 0 mr = 9 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1797 time to turn everything in is 0.5400000 number of dielectric boundary points 25100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19761 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) : 0.5610275 object centre at (A) : -5.313500 59.74750 14.12900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4864965E-02 -3.5727618E-03 midg,1,midg; midg,igrid,midg -4.9930844E-03 9.3891518E-03 1,midg,midg; igrid,midg,midg -7.0051191E-04 -8.1291208E-03 gauss-seidel spectral radius is 0.9982576 estimated iterations to convergence 190 setup time was (sec) 0.8400000 now iterating at: 00:49:10 rms-change max change #iterations 3.370466 164.1747 at 10iterations 1.420209 63.63496 at 20iterations 0.6037419 23.51235 at 30iterations 0.2566880 9.599676 at 40iterations 0.1093138 4.036760 at 50iterations 4.6656314E-02 1.707970 at 60iterations 1.9928098E-02 0.7923794 at 70iterations 8.6009307E-03 0.3140526 at 80iterations 3.7633784E-03 0.1399460 at 90iterations 1.7019378E-03 7.5447083E-02 at 100iterations 8.2001823E-04 3.7723541E-02 at 110iterations 4.1802009E-04 2.0933151E-02 at 120iterations finished qdiffx linear iterations at : 00:49:18 total time elapsed so far: 8.920000 # loops : 120 mean,max change (kT/e) : 4.1802009E-04 2.0933151E-02 energy calculations done at 8.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.090000 DelPhi exited at 00:49:18 9.096u 0.285s 0:09.79 95.7% 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 00:49:18 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2714 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -0.2720 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: 2.524624 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): -37.04100 26.41400 ymin,ymax (A): 32.59500 86.90000 zmin,zma (A): -7.287000 35.54500 x,y,z range (A): 63.45500 54.30500 42.83200 scale (grids/A): 2.524624 object centre (A): -5.313500 59.74750 14.12900 number of atom coordinates read : 2714 total number of charged atoms : 2561 net assigned charge : 4.040014 assigned positive charge : 409.1027 centred at (gu) : 101.7898 91.87383 89.45339 assigned negative charge : -405.0633 centred at (gu) : 100.7710 91.41029 90.33546 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 142937 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22594 grid for indexing accessible points = 1.400000 m= 66633 mr = 104642 m= 19354 mr = 53872 m= 3345 mr = 15030 m= 255 mr = 2318 m= 2 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 5889 time to turn everything in is 1.330000 number of dielectric boundary points 56533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 20475 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) : 1.683082 object centre at (A) : -5.313500 59.74750 14.12900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1802321 -4.3677714E-02 midg,1,midg; midg,igrid,midg -0.1105645 7.5112201E-02 1,midg,midg; igrid,midg,midg 8.9794546E-02 -0.2283100 gauss-seidel spectral radius is 0.9991470 estimated iterations to convergence 270 setup time was (sec) 1.650000 now iterating at: 00:49:20 rms-change max change #iterations 8.435880 332.7074 at 10iterations 4.681211 130.9226 at 20iterations 2.596942 59.10829 at 30iterations 1.435613 28.22662 at 40iterations 0.7930785 16.20145 at 50iterations 0.4373109 9.523041 at 60iterations 0.2412371 5.312637 at 70iterations 0.1332656 3.192745 at 80iterations 7.3611096E-02 1.615223 at 90iterations 4.0612306E-02 0.8356228 at 100iterations 2.2479661E-02 0.4924622 at 110iterations 1.2498322E-02 0.2580042 at 120iterations 6.9938325E-03 0.1565399 at 130iterations 3.9559142E-03 0.1007423 at 140iterations 2.2837480E-03 5.8074951E-02 at 150iterations 1.3675158E-03 3.4950256E-02 at 160iterations 8.5181597E-04 2.6020050E-02 at 170iterations 5.5686553E-04 1.6300201E-02 at 180iterations finished qdiffx linear iterations at : 00:49:33 total time elapsed so far: 14.68000 # loops : 180 mean,max change (kT/e) : 5.5686553E-04 1.6300201E-02 energy calculations done at 14.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.85000 DelPhi exited at 00:49:34 14.854u 0.284s 0:15.50 97.6% 0+0k 0+0io 0pf+0w