Sun Oct 9 16:41:05 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 Sun Oct 9 2011 at 16:41:05 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3578 !!! WARNING: GLM 45 has a net charge of -0.0940 !!! WARNING: GLM 117 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5853242 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): -74.43501 -17.42700 ymin,ymax (A): -11.77100 49.05000 zmin,zma (A): -70.51400 -9.960000 x,y,z range (A): 57.00800 60.82100 60.55400 scale (grids/A): 0.5853242 object centre (A): -45.93100 18.63950 -40.23700 number of atom coordinates read : 3578 total number of charged atoms : 3418 net assigned charge : -0.6879877 assigned positive charge : 532.9779 centred at (gu) : 89.62561 89.61819 92.06078 assigned negative charge : -533.6679 centred at (gu) : 89.63007 89.60857 91.90694 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8287 nv = 96 ne = 84 npr = 68870 no. pairs analyzed = 68870 no. exposed pairs = 5327 no. arc points = 37772 no. surface atoms = 1744 nbur = 1834 mkacc time = 0.1800000 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 = 1.456000 m= 425 mr = 3862 m= 0 mr = 28 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.4400000 number of dielectric boundary points 4822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3768 ## 395 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 10487 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2140033E-09 7.2926620E-09 midg,1,midg; midg,igrid,midg -6.4354944E-10 1.2108717E-11 1,midg,midg; igrid,midg,midg -1.5995218E-10 -3.9160877E-10 gauss-seidel spectral radius is 0.9850008 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 16:41:05 rms-change max change #iterations 0.1087824 16.07103 at 10iterations 8.7462021E-03 1.399014 at 20iterations 6.9424039E-04 9.2578888E-02 at 30iterations 5.6045330E-05 7.8086853E-03 at 40iterations 5.0169747E-06 7.4386597E-04 at 50iterations finished qdiffx linear iterations at : 16:41:08 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 5.0169747E-06 7.4386597E-04 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 16:41:09 3.397u 0.139s 0:03.84 91.6% 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 16:41:09 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3578 !!! WARNING: GLM 45 has a net charge of -0.0940 !!! WARNING: GLM 117 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.755973 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): -74.43501 -17.42700 ymin,ymax (A): -11.77100 49.05000 zmin,zma (A): -70.51400 -9.960000 x,y,z range (A): 57.00800 60.82100 60.55400 scale (grids/A): 1.755973 object centre (A): -45.93100 18.63950 -40.23700 number of atom coordinates read : 3578 total number of charged atoms : 3418 net assigned charge : -0.6879877 assigned positive charge : 532.9779 centred at (gu) : 88.87574 88.85371 96.18161 assigned negative charge : -533.6679 centred at (gu) : 88.88945 88.82539 95.72065 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 89197 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37772 grid for indexing accessible points = 1.400000 m= 28793 mr = 56720 m= 4059 mr = 18714 m= 198 mr = 2065 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 44714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 306 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 26588 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) : 0.5853242 object centre at (A) : -45.93100 18.63950 -40.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1034451E-02 -1.8973298E-02 midg,1,midg; midg,igrid,midg 2.8252879E-03 1.2789135E-03 1,midg,midg; igrid,midg,midg -1.1907704E-03 -7.2512119E-03 gauss-seidel spectral radius is 0.9985308 estimated iterations to convergence 207 setup time was (sec) 0.9000000 now iterating at: 16:41:10 rms-change max change #iterations 4.340297 199.8965 at 10iterations 1.958519 61.33954 at 20iterations 0.8852235 32.27596 at 30iterations 0.4020467 13.77827 at 40iterations 0.1828928 5.493872 at 50iterations 8.3361290E-02 2.602348 at 60iterations 3.7728719E-02 1.073103 at 70iterations 1.7183222E-02 0.5638180 at 80iterations 7.8069484E-03 0.2372627 at 90iterations 3.5558729E-03 0.1105814 at 100iterations 1.6221077E-03 4.9658775E-02 at 110iterations 7.3930994E-04 2.2453308E-02 at 120iterations finished qdiffx linear iterations at : 16:41:17 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 7.3930994E-04 2.2453308E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 16:41:17 8.132u 0.191s 0:08.63 96.4% 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 16:41:17 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3578 !!! WARNING: GLM 45 has a net charge of -0.0940 !!! WARNING: GLM 117 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.633959 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): -74.43501 -17.42700 ymin,ymax (A): -11.77100 49.05000 zmin,zma (A): -70.51400 -9.960000 x,y,z range (A): 57.00800 60.82100 60.55400 scale (grids/A): 2.633959 object centre (A): -45.93100 18.63950 -40.23700 number of atom coordinates read : 3578 total number of charged atoms : 3418 net assigned charge : -0.6879877 assigned positive charge : 532.9779 centred at (gu) : 88.31342 88.28029 99.27206 assigned negative charge : -533.6679 centred at (gu) : 88.33408 88.23797 98.58080 start vw surface at 0.2100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 206487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37772 grid for indexing accessible points = 1.400000 m= 94295 mr = 139995 m= 31328 mr = 70877 m= 6703 mr = 23013 m= 736 mr = 4398 m= 21 mr = 379 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.540000 number of dielectric boundary points 100905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 27337 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) : 1.755973 object centre at (A) : -45.93100 18.63950 -40.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4372799 -0.1791160 midg,1,midg; midg,igrid,midg -0.1303890 -0.1489731 1,midg,midg; igrid,midg,midg -3.5834711E-02 -0.1276491 gauss-seidel spectral radius is 0.9992774 estimated iterations to convergence 294 setup time was (sec) 1.860000 now iterating at: 16:41:19 rms-change max change #iterations 11.09476 324.3808 at 10iterations 6.701085 161.0751 at 20iterations 4.006107 90.73105 at 30iterations 2.374503 49.48080 at 40iterations 1.399852 29.91220 at 50iterations 0.8238607 16.78501 at 60iterations 0.4829120 9.186233 at 70iterations 0.2822196 5.518009 at 80iterations 0.1642502 3.079746 at 90iterations 9.5534869E-02 1.721195 at 100iterations 5.5550437E-02 1.048645 at 110iterations 3.2304466E-02 0.5887889 at 120iterations 1.8764470E-02 0.3580995 at 130iterations 1.0864115E-02 0.2301484 at 140iterations 6.3022580E-03 0.1170366 at 150iterations 3.6468678E-03 6.6283226E-02 at 160iterations 2.1143986E-03 3.5804749E-02 at 170iterations 1.2261916E-03 2.2451401E-02 at 180iterations finished qdiffx linear iterations at : 16:41:29 total time elapsed so far: 11.48000 # loops : 180 mean,max change (kT/e) : 1.2261916E-03 2.2451401E-02 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.67000 DelPhi exited at 16:41:29 11.669u 0.177s 0:12.12 97.6% 0+0k 0+0io 0pf+0w