Sun Oct 9 20:54:06 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 20:54:06 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3147 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 has a net charge of 1.4000 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: 0.6673665 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): 45.30900 98.19300 ymin,ymax (A): 2.810000 56.15400 zmin,zma (A): 15.28200 67.79000 x,y,z range (A): 52.88400 53.34400 52.50800 scale (grids/A): 0.6673665 object centre (A): 71.75100 29.48200 41.53600 number of atom coordinates read : 3147 total number of charged atoms : 3000 net assigned charge : 9.700016 assigned positive charge : 478.1208 centred at (gu) : 90.50298 88.60769 90.52407 assigned negative charge : -468.4222 centred at (gu) : 90.40553 88.49899 90.51738 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 9598 nv = 96 ne = 84 npr = 62238 no. pairs analyzed = 62238 no. exposed pairs = 3955 no. arc points = 28537 no. surface atoms = 1318 nbur = 1829 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 571 mr = 5245 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.2300000 number of dielectric boundary points 4845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2768 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 11230 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5603153E-08 3.5792912E-08 midg,1,midg; midg,igrid,midg -2.3661624E-09 4.6125621E-08 1,midg,midg; igrid,midg,midg 2.0048738E-09 6.4296621E-08 gauss-seidel spectral radius is 0.9884194 estimated iterations to convergence 76 setup time was (sec) 0.4200000 now iterating at: 20:54:07 rms-change max change #iterations 0.1969069 28.57454 at 10iterations 2.1421531E-02 2.635872 at 20iterations 2.3210659E-03 0.2864151 at 30iterations 2.5866783E-04 3.2133102E-02 at 40iterations 2.7887747E-05 3.4868717E-03 at 50iterations finished qdiffx linear iterations at : 20:54:10 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 2.7887747E-05 3.4868717E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 20:54:10 3.472u 0.174s 0:03.93 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 Sun Oct 9 2011 at 20:54:10 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3147 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 has a net charge of 1.4000 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: 2.002100 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): 45.30900 98.19300 ymin,ymax (A): 2.810000 56.15400 zmin,zma (A): 15.28200 67.79000 x,y,z range (A): 52.88400 53.34400 52.50800 scale (grids/A): 2.002100 object centre (A): 71.75100 29.48200 41.53600 number of atom coordinates read : 3147 total number of charged atoms : 3000 net assigned charge : 9.700016 assigned positive charge : 478.1208 centred at (gu) : 91.50826 85.82220 91.57134 assigned negative charge : -468.4222 centred at (gu) : 91.21613 85.49668 91.55199 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 102802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28537 grid for indexing accessible points = 1.400000 m= 37671 mr = 71252 m= 6751 mr = 27642 m= 572 mr = 4287 m= 21 mr = 291 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2157 time to turn everything in is 0.4900000 number of dielectric boundary points 44345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 23765 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) : 0.6673665 object centre at (A) : 71.75100 29.48200 41.53600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9578922E-03 -1.3514378E-02 midg,1,midg; midg,igrid,midg 0.1022524 7.3496476E-02 1,midg,midg; igrid,midg,midg 1.3552925E-02 3.6879398E-02 gauss-seidel spectral radius is 0.9988179 estimated iterations to convergence 230 setup time was (sec) 0.7200000 now iterating at: 20:54:11 rms-change max change #iterations 5.212398 180.9544 at 10iterations 2.576824 89.31174 at 20iterations 1.264600 35.15261 at 30iterations 0.6242869 18.24211 at 40iterations 0.3073176 9.166509 at 50iterations 0.1514491 4.307305 at 60iterations 7.4964970E-02 2.110392 at 70iterations 3.6899570E-02 0.9868002 at 80iterations 1.8223539E-02 0.4952469 at 90iterations 8.9973295E-03 0.2398033 at 100iterations 4.4334373E-03 0.1145926 at 110iterations 2.1910272E-03 5.8401108E-02 at 120iterations finished qdiffx linear iterations at : 20:54:18 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 2.1910272E-03 5.8401108E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 20:54:19 8.177u 0.211s 0:08.66 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 20:54:19 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3147 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 has a net charge of 1.4000 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: 3.003149 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): 45.30900 98.19300 ymin,ymax (A): 2.810000 56.15400 zmin,zma (A): 15.28200 67.79000 x,y,z range (A): 52.88400 53.34400 52.50800 scale (grids/A): 3.003149 object centre (A): 71.75100 29.48200 41.53600 number of atom coordinates read : 3147 total number of charged atoms : 3000 net assigned charge : 9.700016 assigned positive charge : 478.1208 centred at (gu) : 92.26209 83.73306 92.35683 assigned negative charge : -468.4222 centred at (gu) : 91.82393 83.24502 92.32780 start vw surface at 0.1100000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 237716 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28537 grid for indexing accessible points = 1.400000 m= 120520 mr = 172461 m= 45198 mr = 98415 m= 12347 mr = 36146 m= 2310 mr = 9434 m= 270 mr = 1635 m= 5 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 7373 time to turn everything in is 1.310000 number of dielectric boundary points 100097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 24000 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) : 2.002100 object centre at (A) : 71.75100 29.48200 41.53600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1502611 -0.3313159 midg,1,midg; midg,igrid,midg 0.6965794 0.5072303 1,midg,midg; igrid,midg,midg 0.2681901 0.4936527 gauss-seidel spectral radius is 0.9993260 estimated iterations to convergence 304 setup time was (sec) 1.560000 now iterating at: 20:54:21 rms-change max change #iterations 12.04518 474.7244 at 10iterations 7.248366 188.5740 at 20iterations 4.338758 89.35738 at 30iterations 2.603346 50.23358 at 40iterations 1.548966 30.51747 at 50iterations 0.9205366 20.75542 at 60iterations 0.5471466 11.34270 at 70iterations 0.3248937 5.124395 at 80iterations 0.1923149 3.387693 at 90iterations 0.1138366 1.887294 at 100iterations 6.7382410E-02 1.238268 at 110iterations 3.9836008E-02 0.6069040 at 120iterations 2.3541952E-02 0.3700197 at 130iterations 1.3923699E-02 0.2420235 at 140iterations 8.2161408E-03 0.1308517 at 150iterations 4.8459680E-03 7.5006485E-02 at 160iterations 2.8648924E-03 4.3075562E-02 at 170iterations 1.6937585E-03 2.7495384E-02 at 180iterations finished qdiffx linear iterations at : 20:54:33 total time elapsed so far: 13.49000 # loops : 180 mean,max change (kT/e) : 1.6937585E-03 2.7495384E-02 energy calculations done at 13.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.62000 DelPhi exited at 20:54:33 13.625u 0.207s 0:14.10 98.0% 0+0k 0+0io 0pf+0w