Sun Oct 9 21:52:42 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 21:52:42 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 = 3161 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 422 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6614887 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): 45.36100 98.23600 ymin,ymax (A): 3.472000 57.29000 zmin,zma (A): 15.14700 68.21400 x,y,z range (A): 52.87500 53.81800 53.06699 scale (grids/A): 0.6614887 object centre (A): 71.79850 30.38100 41.68050 number of atom coordinates read : 3161 total number of charged atoms : 3013 net assigned charge : 7.800018 assigned positive charge : 482.1107 centred at (gu) : 90.51487 88.42740 90.75153 assigned negative charge : -474.3121 centred at (gu) : 90.43694 88.36607 90.74465 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9515 nv = 96 ne = 84 npr = 62278 no. pairs analyzed = 62278 no. exposed pairs = 4086 no. arc points = 29139 no. surface atoms = 1366 nbur = 1795 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 526 mr = 5121 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3400000 number of dielectric boundary points 4865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2781 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 11070 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6375953E-08 2.6129772E-08 midg,1,midg; midg,igrid,midg 6.8420354E-09 2.6140487E-08 1,midg,midg; igrid,midg,midg 1.0626292E-09 4.4573525E-08 gauss-seidel spectral radius is 0.9882147 estimated iterations to convergence 75 setup time was (sec) 0.5700000 now iterating at: 21:52:43 rms-change max change #iterations 0.1892833 23.41217 at 10iterations 2.0253167E-02 2.571663 at 20iterations 2.1852253E-03 0.2543335 at 30iterations 2.3294891E-04 3.2203674E-02 at 40iterations 2.5475043E-05 3.2234192E-03 at 50iterations finished qdiffx linear iterations at : 21:52:45 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 2.5475043E-05 3.2234192E-03 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 21:52:46 3.197u 0.121s 0:03.64 90.9% 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 Sun Oct 9 2011 at 21:52:46 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 = 3161 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 422 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.984466 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): 45.36100 98.23600 ymin,ymax (A): 3.472000 57.29000 zmin,zma (A): 15.14700 68.21400 x,y,z range (A): 52.87500 53.81800 53.06699 scale (grids/A): 1.984466 object centre (A): 71.79850 30.38100 41.68050 number of atom coordinates read : 3161 total number of charged atoms : 3013 net assigned charge : 7.800018 assigned positive charge : 482.1107 centred at (gu) : 91.54336 85.28117 92.25376 assigned negative charge : -474.3121 centred at (gu) : 91.31061 85.09784 92.23367 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 101781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29139 grid for indexing accessible points = 1.400000 m= 36853 mr = 70030 m= 6242 mr = 26699 m= 472 mr = 3794 m= 10 mr = 168 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1028 time to turn everything in is 0.6700000 number of dielectric boundary points 44668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 23804 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) : 0.6614887 object centre at (A) : 71.79850 30.38100 41.68050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4693858E-03 -1.8642109E-02 midg,1,midg; midg,igrid,midg 9.6737817E-02 6.3227117E-02 1,midg,midg; igrid,midg,midg 8.5184323E-03 4.0037584E-02 gauss-seidel spectral radius is 0.9987993 estimated iterations to convergence 228 setup time was (sec) 0.9400000 now iterating at: 21:52:47 rms-change max change #iterations 5.153481 182.4222 at 10iterations 2.524323 77.29003 at 20iterations 1.232584 41.35076 at 30iterations 0.6061541 17.63800 at 40iterations 0.2965822 9.223007 at 50iterations 0.1458892 3.885239 at 60iterations 7.1522370E-02 1.940468 at 70iterations 3.5087008E-02 0.9247837 at 80iterations 1.7198408E-02 0.4549408 at 90iterations 8.4460769E-03 0.2238150 at 100iterations 4.1479021E-03 0.1157522 at 110iterations 2.0308290E-03 5.8654785E-02 at 120iterations finished qdiffx linear iterations at : 21:52:53 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 2.0308290E-03 5.8654785E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 21:52:54 7.487u 0.150s 0:07.98 95.6% 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 21:52:54 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 = 3161 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 422 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.976699 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): 45.36100 98.23600 ymin,ymax (A): 3.472000 57.29000 zmin,zma (A): 15.14700 68.21400 x,y,z range (A): 52.87500 53.81800 53.06699 scale (grids/A): 2.976699 object centre (A): 71.79850 30.38100 41.68050 number of atom coordinates read : 3161 total number of charged atoms : 3013 net assigned charge : 7.800018 assigned positive charge : 482.1107 centred at (gu) : 92.31495 82.92164 93.38056 assigned negative charge : -474.3121 centred at (gu) : 91.96584 82.64671 93.35071 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 235105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29139 grid for indexing accessible points = 1.400000 m= 118128 mr = 169585 m= 43813 mr = 95937 m= 11441 mr = 34574 m= 2036 mr = 8437 m= 177 mr = 1373 m= 0 mr = 82 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 3169 time to turn everything in is 1.720000 number of dielectric boundary points 100712 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 24104 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) : 1.984466 object centre at (A) : 71.79850 30.38100 41.68050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6217273E-02 -0.4536782 midg,1,midg; midg,igrid,midg 0.8024954 0.5988852 1,midg,midg; igrid,midg,midg 0.2885397 0.5396393 gauss-seidel spectral radius is 0.9993237 estimated iterations to convergence 303 setup time was (sec) 2.010000 now iterating at: 21:52:56 rms-change max change #iterations 11.95794 410.0004 at 10iterations 7.236173 152.3100 at 20iterations 4.333323 85.62650 at 30iterations 2.592330 45.50419 at 40iterations 1.550071 25.57944 at 50iterations 0.9237482 16.82950 at 60iterations 0.5484411 9.552140 at 70iterations 0.3255060 5.449737 at 80iterations 0.1925297 3.179626 at 90iterations 0.1139548 1.700809 at 100iterations 6.7472734E-02 1.210983 at 110iterations 3.9867420E-02 0.6624241 at 120iterations 2.3584967E-02 0.4146767 at 130iterations 1.3909620E-02 0.2387352 at 140iterations 8.2202349E-03 0.1377344 at 150iterations 4.8471009E-03 7.9902053E-02 at 160iterations 2.8574748E-03 4.4390678E-02 at 170iterations 1.6924548E-03 2.8282166E-02 at 180iterations finished qdiffx linear iterations at : 21:53:06 total time elapsed so far: 12.27000 # loops : 180 mean,max change (kT/e) : 1.6924548E-03 2.8282166E-02 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 21:53:07 12.450u 0.164s 0:12.98 97.1% 0+0k 0+0io 0pf+0w