Tue Oct 11 03:20:17 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 03:20:17 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5660408 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): -10.97800 43.93200 ymin,ymax (A): 14.35300 75.68200 zmin,zma (A): 39.71800 102.6110 x,y,z range (A): 54.91000 61.32900 62.89300 scale (grids/A): 0.5660408 object centre (A): 16.47700 45.01750 71.16451 number of atom coordinates read : 3396 total number of charged atoms : 3255 net assigned charge : -7.518967 assigned positive charge : 515.0985 centred at (gu) : 88.27016 87.85912 88.15025 assigned negative charge : -522.6188 centred at (gu) : 88.29275 87.84090 88.14230 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7024 nv = 96 ne = 84 npr = 69281 no. pairs analyzed = 69281 no. exposed pairs = 4326 no. arc points = 30588 no. surface atoms = 1453 nbur = 1943 mkacc time = 0.1700000 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 = 1.512000 m= 330 mr = 3603 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3104 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9078 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7163312E-09 -5.6251398E-10 midg,1,midg; midg,igrid,midg -2.1173432E-09 -4.2976905E-10 1,midg,midg; igrid,midg,midg -9.2647762E-10 -8.9818358E-10 gauss-seidel spectral radius is 0.9839299 estimated iterations to convergence 65 setup time was (sec) 0.6300000 now iterating at: 03:20:18 rms-change max change #iterations 9.8576397E-02 13.79069 at 10iterations 7.2470563E-03 1.214390 at 20iterations 6.3381734E-04 9.9861145E-02 at 30iterations 1.1419899E-04 1.7985344E-02 at 40iterations 3.4858800E-05 6.5093040E-03 at 50iterations finished qdiffx linear iterations at : 03:20:21 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 3.4858800E-05 6.5093040E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 03:20:22 3.472u 0.134s 0:04.14 86.9% 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 Tue Oct 11 2011 at 03:20:22 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.698122 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): -10.97800 43.93200 ymin,ymax (A): 14.35300 75.68200 zmin,zma (A): 39.71800 102.6110 x,y,z range (A): 54.91000 61.32900 62.89300 scale (grids/A): 1.698122 object centre (A): 16.47700 45.01750 71.16451 number of atom coordinates read : 3396 total number of charged atoms : 3255 net assigned charge : -7.518967 assigned positive charge : 515.0985 centred at (gu) : 84.80954 83.57624 84.44964 assigned negative charge : -522.6188 centred at (gu) : 84.87786 83.52238 84.42648 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 75968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30588 grid for indexing accessible points = 1.400000 m= 26191 mr = 50910 m= 3404 mr = 18685 m= 115 mr = 1770 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 541 time to turn everything in is 0.6100000 number of dielectric boundary points 34296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 299 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 25103 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) : 0.5660408 object centre at (A) : 16.47700 45.01750 71.16451 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7193396E-02 3.3939660E-02 midg,1,midg; midg,igrid,midg -6.5547884E-03 3.7687933E-03 1,midg,midg; igrid,midg,midg -4.8820591E-03 4.9852661E-04 gauss-seidel spectral radius is 0.9983626 estimated iterations to convergence 196 setup time was (sec) 0.8900000 now iterating at: 03:20:23 rms-change max change #iterations 3.972107 190.3917 at 10iterations 1.716515 62.19007 at 20iterations 0.7474263 24.93682 at 30iterations 0.3255368 10.43822 at 40iterations 0.1418306 4.500589 at 50iterations 6.1643969E-02 1.989738 at 60iterations 2.6957089E-02 0.9330316 at 70iterations 1.1772211E-02 0.4409635 at 80iterations 5.1366081E-03 0.1768036 at 90iterations 2.2702010E-03 8.0030441E-02 at 100iterations 1.0115817E-03 3.2230377E-02 at 110iterations 4.6253036E-04 1.5641212E-02 at 120iterations finished qdiffx linear iterations at : 03:20:29 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 4.6253036E-04 1.5641212E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 03:20:30 7.553u 0.191s 0:08.03 96.3% 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 03:20:30 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.547184 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): -10.97800 43.93200 ymin,ymax (A): 14.35300 75.68200 zmin,zma (A): 39.71800 102.6110 x,y,z range (A): 54.91000 61.32900 62.89300 scale (grids/A): 2.547184 object centre (A): 16.47700 45.01750 71.16451 number of atom coordinates read : 3396 total number of charged atoms : 3255 net assigned charge : -7.518967 assigned positive charge : 515.0985 centred at (gu) : 82.21422 80.36432 81.67428 assigned negative charge : -522.6188 centred at (gu) : 82.31664 80.28342 81.63963 start vw surface at 0.1900000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175882 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30588 grid for indexing accessible points = 1.400000 m= 86230 mr = 124245 m= 29155 mr = 68985 m= 5495 mr = 22812 m= 525 mr = 3664 m= 15 mr = 265 m= 0 mr = 2 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 1611 time to turn everything in is 1.430000 number of dielectric boundary points 77329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 26021 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) : 1.698122 object centre at (A) : 16.47700 45.01750 71.16451 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3489895 0.8805410 midg,1,midg; midg,igrid,midg -1.2681301E-03 0.2441026 1,midg,midg; igrid,midg,midg -4.0703688E-02 -1.8524406E-02 gauss-seidel spectral radius is 0.9992033 estimated iterations to convergence 280 setup time was (sec) 1.740000 now iterating at: 03:20:32 rms-change max change #iterations 10.01072 292.8979 at 10iterations 5.760601 170.0383 at 20iterations 3.293813 80.41942 at 30iterations 1.879010 42.62516 at 40iterations 1.065957 23.13197 at 50iterations 0.6037467 13.97084 at 60iterations 0.3414634 6.813421 at 70iterations 0.1930592 3.472486 at 80iterations 0.1089500 2.268661 at 90iterations 6.1289180E-02 1.152554 at 100iterations 3.4616400E-02 0.7009945 at 110iterations 1.9494439E-02 0.3522979 at 120iterations 1.0984603E-02 0.2145209 at 130iterations 6.1946209E-03 0.1168613 at 140iterations 3.4907889E-03 6.8338394E-02 at 150iterations 1.9672976E-03 4.1650772E-02 at 160iterations 1.1151236E-03 2.2454739E-02 at 170iterations 6.3639163E-04 1.1576653E-02 at 180iterations finished qdiffx linear iterations at : 03:20:42 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 6.3639163E-04 1.1576653E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 03:20:43 12.796u 0.170s 0:13.28 97.5% 0+0k 0+0io 0pf+0w