Tue Oct 11 06:46:47 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 06:46:47 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3505 !!! WARNING: HIR 44 has a net charge of 0.5140 !!! WARNING: SEP 194 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: 0.5779127 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): -23.81800 34.24000 ymin,ymax (A): -42.63800 18.96300 zmin,zma (A): 37.07000 87.16700 x,y,z range (A): 58.05800 61.60100 50.09700 scale (grids/A): 0.5779127 object centre (A): 5.211001 -11.83750 62.11850 number of atom coordinates read : 3505 total number of charged atoms : 3369 net assigned charge : -7.460977 assigned positive charge : 527.9706 centred at (gu) : 87.30945 89.64200 90.33788 assigned negative charge : -535.4328 centred at (gu) : 87.34306 89.87160 90.21674 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7832 nv = 96 ne = 84 npr = 69472 no. pairs analyzed = 69472 no. exposed pairs = 4747 no. arc points = 32879 no. surface atoms = 1581 nbur = 1924 mkacc time = 0.1200000 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 = 1.484000 m= 347 mr = 3943 m= 0 mr = 11 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3298 ## 361 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9958 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2185353E-09 1.4990748E-09 midg,1,midg; midg,igrid,midg 4.2859893E-09 -6.7454735E-09 1,midg,midg; igrid,midg,midg -1.3135245E-09 -1.2884579E-09 gauss-seidel spectral radius is 0.9845968 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 06:46:47 rms-change max change #iterations 0.1091118 17.67197 at 10iterations 8.9058550E-03 1.148154 at 20iterations 1.0491085E-03 0.1356049 at 30iterations 2.5428546E-04 2.7328491E-02 at 40iterations 7.8517362E-05 8.1863403E-03 at 50iterations finished qdiffx linear iterations at : 06:46:50 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 7.8517362E-05 8.1863403E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 06:46:51 3.414u 0.170s 0:03.94 90.8% 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 06:46:51 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3505 !!! WARNING: HIR 44 has a net charge of 0.5140 !!! WARNING: SEP 194 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: 1.733738 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): -23.81800 34.24000 ymin,ymax (A): -42.63800 18.96300 zmin,zma (A): 37.07000 87.16700 x,y,z range (A): 58.05800 61.60100 50.09700 scale (grids/A): 1.733738 object centre (A): 5.211001 -11.83750 62.11850 number of atom coordinates read : 3505 total number of charged atoms : 3369 net assigned charge : -7.460977 assigned positive charge : 527.9706 centred at (gu) : 81.92735 88.92474 91.01303 assigned negative charge : -535.4328 centred at (gu) : 82.02882 89.61440 90.64973 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 85171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32879 grid for indexing accessible points = 1.400000 m= 27359 mr = 56783 m= 3017 mr = 18408 m= 94 mr = 1407 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 39040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 309 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 26195 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) : 0.5779127 object centre at (A) : 5.211001 -11.83750 62.11850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3702525E-02 1.1395098E-02 midg,1,midg; midg,igrid,midg 4.9382769E-02 -2.5733875E-02 1,midg,midg; igrid,midg,midg -1.8462412E-02 -1.1733273E-02 gauss-seidel spectral radius is 0.9984569 estimated iterations to convergence 202 setup time was (sec) 0.6200000 now iterating at: 06:46:52 rms-change max change #iterations 4.197451 165.7942 at 10iterations 1.869581 74.95471 at 20iterations 0.8317164 26.98267 at 30iterations 0.3711860 11.42979 at 40iterations 0.1659957 5.615094 at 50iterations 7.4403271E-02 2.541998 at 60iterations 3.3256765E-02 1.095709 at 70iterations 1.4854938E-02 0.4561634 at 80iterations 6.6784462E-03 0.2153144 at 90iterations 3.0243837E-03 0.1118563 at 100iterations 1.3883068E-03 4.6682358E-02 at 110iterations 6.4822205E-04 1.8138081E-02 at 120iterations finished qdiffx linear iterations at : 06:46:59 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 6.4822205E-04 1.8138081E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 06:46:59 7.831u 0.202s 0:08.34 96.2% 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 06:46:59 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3505 !!! WARNING: HIR 44 has a net charge of 0.5140 !!! WARNING: SEP 194 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: 2.600607 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): -23.81800 34.24000 ymin,ymax (A): -42.63800 18.96300 zmin,zma (A): 37.07000 87.16700 x,y,z range (A): 58.05800 61.60100 50.09700 scale (grids/A): 2.600607 object centre (A): 5.211001 -11.83750 62.11850 number of atom coordinates read : 3505 total number of charged atoms : 3369 net assigned charge : -7.460977 assigned positive charge : 527.9706 centred at (gu) : 77.89096 88.38696 91.51942 assigned negative charge : -535.4328 centred at (gu) : 78.04309 89.42151 90.97432 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 197522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32879 grid for indexing accessible points = 1.400000 m= 92984 mr = 139103 m= 27821 mr = 72643 m= 4748 mr = 20425 m= 399 mr = 3038 m= 13 mr = 167 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 88112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 26930 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) : 1.733738 object centre at (A) : 5.211001 -11.83750 62.11850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1812239 0.1590096 midg,1,midg; midg,igrid,midg 0.8549337 -0.1195262 1,midg,midg; igrid,midg,midg -0.2508093 -0.1404647 gauss-seidel spectral radius is 0.9992437 estimated iterations to convergence 287 setup time was (sec) 1.260000 now iterating at: 06:47:01 rms-change max change #iterations 10.61537 282.8877 at 10iterations 6.310968 144.2580 at 20iterations 3.706029 86.58815 at 30iterations 2.166603 47.11834 at 40iterations 1.259504 25.72919 at 50iterations 0.7299879 14.79993 at 60iterations 0.4216702 8.826766 at 70iterations 0.2430891 4.467991 at 80iterations 0.1402485 2.703201 at 90iterations 8.0573723E-02 1.593704 at 100iterations 4.6233121E-02 0.8272552 at 110iterations 2.6578551E-02 0.4523516 at 120iterations 1.5232801E-02 0.2860909 at 130iterations 8.7417485E-03 0.1555295 at 140iterations 5.0144549E-03 0.1077614 at 150iterations 2.8793192E-03 5.8289051E-02 at 160iterations 1.6620115E-03 3.0012131E-02 at 170iterations 9.5996610E-04 1.8220901E-02 at 180iterations finished qdiffx linear iterations at : 06:47:12 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 9.5996610E-04 1.8220901E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 06:47:13 12.973u 0.221s 0:13.71 96.2% 0+0k 0+0io 0pf+0w