Tue Oct 11 08:24:28 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 Tue Oct 11 2011 at 08:24:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 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: 0.6076330 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): -20.64800 31.02100 ymin,ymax (A): -15.47700 36.34500 zmin,zma (A): -24.05900 34.52900 x,y,z range (A): 51.66900 51.82200 58.58800 scale (grids/A): 0.6076330 object centre (A): 5.186501 10.43400 5.235000 number of atom coordinates read : 3141 total number of charged atoms : 3003 net assigned charge : -6.499979 assigned positive charge : 466.6339 centred at (gu) : 91.26289 89.99673 91.60714 assigned negative charge : -473.1350 centred at (gu) : 91.27100 90.08009 91.61242 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7841 nv = 96 ne = 84 npr = 63818 no. pairs analyzed = 63818 no. exposed pairs = 3939 no. arc points = 27242 no. surface atoms = 1344 nbur = 1797 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 4312 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2842 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9752 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2947497E-09 -5.4473261E-09 midg,1,midg; midg,igrid,midg 1.0882707E-09 -8.2311660E-09 1,midg,midg; igrid,midg,midg -2.3497411E-09 -5.2600106E-09 gauss-seidel spectral radius is 0.9860277 estimated iterations to convergence 69 setup time was (sec) 0.7100000 now iterating at: 08:24:29 rms-change max change #iterations 0.1254819 19.62906 at 10iterations 1.1166327E-02 1.685658 at 20iterations 1.1804824E-03 0.1644118 at 30iterations 2.6066086E-04 3.3598900E-02 at 40iterations 9.1043359E-05 1.2242198E-02 at 50iterations finished qdiffx linear iterations at : 08:24:32 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 9.1043359E-05 1.2242198E-02 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 08:24:33 4.066u 0.151s 0:04.82 87.3% 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 08:24:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 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: 1.822899 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): -20.64800 31.02100 ymin,ymax (A): -15.47700 36.34500 zmin,zma (A): -24.05900 34.52900 x,y,z range (A): 51.66900 51.82200 58.58800 scale (grids/A): 1.822899 object centre (A): 5.186501 10.43400 5.235000 number of atom coordinates read : 3141 total number of charged atoms : 3003 net assigned charge : -6.499979 assigned positive charge : 466.6339 centred at (gu) : 93.78802 89.98944 94.82063 assigned negative charge : -473.1350 centred at (gu) : 93.81281 90.23943 94.83668 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 85414 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27242 grid for indexing accessible points = 1.400000 m= 30528 mr = 59627 m= 4022 mr = 22331 m= 155 mr = 2275 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 35859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 23497 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) : 0.6076330 object centre at (A) : 5.186501 10.43400 5.235000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2004228E-02 -3.8637355E-02 midg,1,midg; midg,igrid,midg -1.9349415E-03 -2.5231088E-02 1,midg,midg; igrid,midg,midg -6.7157210E-03 -1.5346956E-03 gauss-seidel spectral radius is 0.9985681 estimated iterations to convergence 210 setup time was (sec) 1.140000 now iterating at: 08:24:34 rms-change max change #iterations 4.285203 189.0247 at 10iterations 1.952745 59.70053 at 20iterations 0.9004718 28.72260 at 30iterations 0.4136085 12.17871 at 40iterations 0.1907150 6.397587 at 50iterations 8.7600730E-02 2.612113 at 60iterations 4.0373884E-02 1.199982 at 70iterations 1.8628983E-02 0.6104603 at 80iterations 8.6050732E-03 0.2936325 at 90iterations 4.0008212E-03 0.1259613 at 100iterations 1.9016099E-03 5.8965683E-02 at 110iterations 9.3549839E-04 2.8835297E-02 at 120iterations finished qdiffx linear iterations at : 08:24:42 total time elapsed so far: 9.030000 # loops : 120 mean,max change (kT/e) : 9.3549839E-04 2.8835297E-02 energy calculations done at 9.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.280000 DelPhi exited at 08:24:43 9.284u 0.190s 0:10.40 91.0% 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 08:24:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 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: 2.734349 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): -20.64800 31.02100 ymin,ymax (A): -15.47700 36.34500 zmin,zma (A): -24.05900 34.52900 x,y,z range (A): 51.66900 51.82200 58.58800 scale (grids/A): 2.734349 object centre (A): 5.186501 10.43400 5.235000 number of atom coordinates read : 3141 total number of charged atoms : 3003 net assigned charge : -6.499979 assigned positive charge : 466.6339 centred at (gu) : 95.68179 89.98392 97.23067 assigned negative charge : -473.1350 centred at (gu) : 95.71891 90.35907 97.25479 start vw surface at 0.2100000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 197448 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27242 grid for indexing accessible points = 1.400000 m= 100826 mr = 144327 m= 34059 mr = 82545 m= 6933 mr = 27007 m= 662 mr = 4798 m= 26 mr = 353 m= 0 mr = 7 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.030000 number of dielectric boundary points 80917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 24020 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) : 1.822899 object centre at (A) : 5.186501 10.43400 5.235000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2292862E-02 -0.4198242 midg,1,midg; midg,igrid,midg -3.5186008E-02 -0.2628659 1,midg,midg; igrid,midg,midg -0.1227062 -5.1705442E-02 gauss-seidel spectral radius is 0.9992570 estimated iterations to convergence 290 setup time was (sec) 2.400000 now iterating at: 08:24:46 rms-change max change #iterations 10.26605 434.4480 at 10iterations 6.023053 141.8441 at 20iterations 3.504020 63.59571 at 30iterations 2.030353 38.03792 at 40iterations 1.175247 25.56954 at 50iterations 0.6768601 14.16544 at 60iterations 0.3913633 7.139156 at 70iterations 0.2250697 3.951110 at 80iterations 0.1294249 2.333304 at 90iterations 7.4648000E-02 1.330415 at 100iterations 4.2893343E-02 0.7219334 at 110iterations 2.4673102E-02 0.5006733 at 120iterations 1.4186829E-02 0.2337136 at 130iterations 8.1810048E-03 0.1313803 at 140iterations 4.7435178E-03 8.1176758E-02 at 150iterations 2.7540775E-03 5.4823875E-02 at 160iterations 1.6247567E-03 2.9447556E-02 at 170iterations 9.7976404E-04 1.8992901E-02 at 180iterations finished qdiffx linear iterations at : 08:24:58 total time elapsed so far: 14.52000 # loops : 180 mean,max change (kT/e) : 9.7976404E-04 1.8992901E-02 energy calculations done at 14.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.76000 DelPhi exited at 08:24:58 14.763u 0.190s 0:15.42 96.9% 0+0k 0+0io 0pf+0w