Tue Oct 11 07:55:21 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 07:55:21 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.6384505 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): -24.61200 21.35800 ymin,ymax (A): 4.105000 59.86500 zmin,zma (A): -20.16200 24.79100 x,y,z range (A): 45.97000 55.76000 44.95300 scale (grids/A): 0.6384505 object centre (A): -1.627000 31.98500 2.314501 number of atom coordinates read : 2366 total number of charged atoms : 2239 net assigned charge : 5.025008 assigned positive charge : 358.9355 centred at (gu) : 90.59575 91.13396 89.37759 assigned negative charge : -353.9108 centred at (gu) : 90.40457 91.17796 89.43016 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6375 nv = 96 ne = 84 npr = 48572 no. pairs analyzed = 48572 no. exposed pairs = 2873 no. arc points = 20174 no. surface atoms = 967 nbur = 1399 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 312 mr = 3503 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2017 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7673 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3947270E-08 1.3665742E-09 midg,1,midg; midg,igrid,midg 8.9471115E-09 2.9541529E-09 1,midg,midg; igrid,midg,midg -1.1353877E-08 2.9527021E-08 gauss-seidel spectral radius is 0.9872662 estimated iterations to convergence 72 setup time was (sec) 0.4900000 now iterating at: 07:55:22 rms-change max change #iterations 0.1395982 20.34616 at 10iterations 1.3586492E-02 2.052188 at 20iterations 1.3507552E-03 0.1974611 at 30iterations 1.2991267E-04 1.9121647E-02 at 40iterations 1.3107002E-05 2.0904541E-03 at 50iterations finished qdiffx linear iterations at : 07:55:24 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.3107002E-05 2.0904541E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 07:55:25 3.145u 0.139s 0:03.66 89.3% 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 07:55:25 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 1.915351 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): -24.61200 21.35800 ymin,ymax (A): 4.105000 59.86500 zmin,zma (A): -20.16200 24.79100 x,y,z range (A): 45.97000 55.76000 44.95300 scale (grids/A): 1.915351 object centre (A): -1.627000 31.98500 2.314501 number of atom coordinates read : 2366 total number of charged atoms : 2239 net assigned charge : 5.025008 assigned positive charge : 358.9355 centred at (gu) : 91.78719 93.40179 88.13245 assigned negative charge : -353.9108 centred at (gu) : 91.21375 93.53365 88.29038 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 68251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20174 grid for indexing accessible points = 1.400000 m= 24234 mr = 47077 m= 3714 mr = 17884 m= 180 mr = 2223 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 485 time to turn everything in is 0.4700000 number of dielectric boundary points 29143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 17628 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) : 0.6384505 object centre at (A) : -1.627000 31.98500 2.314501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8958569E-02 1.1250086E-02 midg,1,midg; midg,igrid,midg 4.7201503E-02 1.2568667E-02 1,midg,midg; igrid,midg,midg -9.9731144E-03 2.2439500E-02 gauss-seidel spectral radius is 0.9986249 estimated iterations to convergence 214 setup time was (sec) 0.7200000 now iterating at: 07:55:26 rms-change max change #iterations 4.103835 201.7455 at 10iterations 1.925215 67.77616 at 20iterations 0.8962676 32.54217 at 30iterations 0.4176561 13.43208 at 40iterations 0.1966623 6.233925 at 50iterations 9.1672748E-02 2.870831 at 60iterations 4.2785041E-02 1.476352 at 70iterations 2.0033684E-02 0.7140355 at 80iterations 9.3259821E-03 0.3305378 at 90iterations 4.3524588E-03 0.1501617 at 100iterations 2.0339761E-03 6.6382885E-02 at 110iterations 9.5229055E-04 3.0091286E-02 at 120iterations finished qdiffx linear iterations at : 07:55:32 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 9.5229055E-04 3.0091286E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 07:55:33 6.927u 0.179s 0:07.52 94.2% 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 07:55:33 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.873027 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): -24.61200 21.35800 ymin,ymax (A): 4.105000 59.86500 zmin,zma (A): -20.16200 24.79100 x,y,z range (A): 45.97000 55.76000 44.95300 scale (grids/A): 2.873027 object centre (A): -1.627000 31.98500 2.314501 number of atom coordinates read : 2366 total number of charged atoms : 2239 net assigned charge : 5.025008 assigned positive charge : 358.9355 centred at (gu) : 92.68075 95.10247 87.19868 assigned negative charge : -353.9108 centred at (gu) : 91.82063 95.30036 87.43547 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 157586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20174 grid for indexing accessible points = 1.400000 m= 79207 mr = 114022 m= 28155 mr = 64722 m= 6746 mr = 22682 m= 885 mr = 4982 m= 39 mr = 551 m= 0 mr = 20 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 1579 time to turn everything in is 1.220000 number of dielectric boundary points 65639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 17910 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) : 1.915351 object centre at (A) : -1.627000 31.98500 2.314501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1991899 0.1454317 midg,1,midg; midg,igrid,midg 0.5885565 4.2832918E-02 1,midg,midg; igrid,midg,midg -5.8276877E-02 0.1506561 gauss-seidel spectral radius is 0.9992471 estimated iterations to convergence 288 setup time was (sec) 1.500000 now iterating at: 07:55:34 rms-change max change #iterations 9.545584 362.8018 at 10iterations 5.512165 144.0163 at 20iterations 3.172927 98.62916 at 30iterations 1.824309 40.76421 at 40iterations 1.044816 22.21810 at 50iterations 0.5986599 12.00088 at 60iterations 0.3428632 6.481041 at 70iterations 0.1960633 4.155931 at 80iterations 0.1121900 2.121513 at 90iterations 6.4082041E-02 1.314822 at 100iterations 3.6629520E-02 0.6875709 at 110iterations 2.0956632E-02 0.3834338 at 120iterations 1.1958415E-02 0.2340622 at 130iterations 6.8453392E-03 0.1264856 at 140iterations 3.9238711E-03 7.3776245E-02 at 150iterations 2.2426175E-03 4.3098450E-02 at 160iterations 1.2798671E-03 2.4993896E-02 at 170iterations 7.3378155E-04 1.2823105E-02 at 180iterations finished qdiffx linear iterations at : 07:55:44 total time elapsed so far: 10.87000 # loops : 180 mean,max change (kT/e) : 7.3378155E-04 1.2823105E-02 energy calculations done at 10.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.05000 DelPhi exited at 07:55:44 11.054u 0.188s 0:11.55 97.2% 0+0k 0+0io 0pf+0w