Sun Oct 9 09:20:12 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 Sun Oct 9 2011 at 09:20:12 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 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: 0.5622325 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): -80.15701 -32.33200 ymin,ymax (A): -36.05900 27.26000 zmin,zma (A): -52.66500 1.113000 x,y,z range (A): 47.82500 63.31900 53.77800 scale (grids/A): 0.5622325 object centre (A): -56.24450 -4.399499 -25.77600 number of atom coordinates read : 2780 total number of charged atoms : 2634 net assigned charge : 2.500015 assigned positive charge : 412.7007 centred at (gu) : 89.57731 88.57149 89.52697 assigned negative charge : -410.2014 centred at (gu) : 89.52776 88.61153 89.59467 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5860 nv = 96 ne = 84 npr = 55327 no. pairs analyzed = 55327 no. exposed pairs = 3681 no. arc points = 25841 no. surface atoms = 1234 nbur = 1546 mkacc time = 0.1600000 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 = 1.540000 m= 263 mr = 2960 m= 0 mr = 18 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2644 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7457 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1456168E-09 -4.2036286E-10 midg,1,midg; midg,igrid,midg 1.0183849E-09 -1.1253615E-10 1,midg,midg; igrid,midg,midg -3.0152919E-10 7.4434092E-10 gauss-seidel spectral radius is 0.9836708 estimated iterations to convergence 64 setup time was (sec) 0.6300000 now iterating at: 09:20:13 rms-change max change #iterations 8.2404025E-02 13.66940 at 10iterations 5.8995876E-03 1.000049 at 20iterations 4.4148500E-04 8.9369774E-02 at 30iterations 4.9600516E-05 9.3908310E-03 at 40iterations 1.1430713E-05 2.5959015E-03 at 50iterations finished qdiffx linear iterations at : 09:20:17 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.1430713E-05 2.5959015E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 09:20:17 4.088u 0.257s 0:04.63 93.5% 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 09:20:17 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 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: 1.686697 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): -80.15701 -32.33200 ymin,ymax (A): -36.05900 27.26000 zmin,zma (A): -52.66500 1.113000 x,y,z range (A): 47.82500 63.31900 53.77800 scale (grids/A): 1.686697 object centre (A): -56.24450 -4.399499 -25.77600 number of atom coordinates read : 2780 total number of charged atoms : 2634 net assigned charge : 2.500015 assigned positive charge : 412.7007 centred at (gu) : 88.73138 85.71415 88.58045 assigned negative charge : -410.2014 centred at (gu) : 88.58307 85.83427 88.78386 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 64489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25841 grid for indexing accessible points = 1.400000 m= 21059 mr = 42867 m= 2513 mr = 14690 m= 87 mr = 1316 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.5700000 number of dielectric boundary points 29268 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 0.7100000 number of grid points assigned charge 20315 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) : 0.5622325 object centre at (A) : -56.24450 -4.399499 -25.77600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2770399E-04 -1.1347905E-02 midg,1,midg; midg,igrid,midg -5.5586696E-03 4.7997092E-03 1,midg,midg; igrid,midg,midg 4.7612628E-03 7.5517609E-03 gauss-seidel spectral radius is 0.9982906 estimated iterations to convergence 192 setup time was (sec) 0.8700000 now iterating at: 09:20:18 rms-change max change #iterations 3.400489 170.4878 at 10iterations 1.448791 53.43428 at 20iterations 0.6176808 21.89786 at 30iterations 0.2633662 9.125835 at 40iterations 0.1127524 4.580785 at 50iterations 4.8211314E-02 1.587899 at 60iterations 2.0658419E-02 0.7222710 at 70iterations 8.8386396E-03 0.2996445 at 80iterations 3.7773089E-03 0.1478834 at 90iterations 1.6183592E-03 6.7081451E-02 at 100iterations 6.9683121E-04 2.5532722E-02 at 110iterations 3.0046620E-04 1.0268807E-02 at 120iterations finished qdiffx linear iterations at : 09:20:26 total time elapsed so far: 9.070000 # loops : 120 mean,max change (kT/e) : 3.0046620E-04 1.0268807E-02 energy calculations done at 9.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.250000 DelPhi exited at 09:20:27 9.250u 0.313s 0:09.82 97.3% 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 Sun Oct 9 2011 at 09:20:27 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 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: 2.530046 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): -80.15701 -32.33200 ymin,ymax (A): -36.05900 27.26000 zmin,zma (A): -52.66500 1.113000 x,y,z range (A): 47.82500 63.31900 53.77800 scale (grids/A): 2.530046 object centre (A): -56.24450 -4.399499 -25.77600 number of atom coordinates read : 2780 total number of charged atoms : 2634 net assigned charge : 2.500015 assigned positive charge : 412.7007 centred at (gu) : 88.09695 83.57117 87.87057 assigned negative charge : -410.2014 centred at (gu) : 87.87454 83.75144 88.17564 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 148827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25841 grid for indexing accessible points = 1.400000 m= 70932 mr = 104578 m= 22361 mr = 56224 m= 4038 mr = 17018 m= 383 mr = 2723 m= 9 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 1.430000 number of dielectric boundary points 65810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 21060 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) : 1.686697 object centre at (A) : -56.24450 -4.399499 -25.77600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8844701E-03 -0.1638352 midg,1,midg; midg,igrid,midg -3.7610255E-02 2.9754635E-02 1,midg,midg; igrid,midg,midg 8.9534603E-02 0.1299431 gauss-seidel spectral radius is 0.9991708 estimated iterations to convergence 274 setup time was (sec) 1.760000 now iterating at: 09:20:29 rms-change max change #iterations 8.661865 277.7029 at 10iterations 4.906834 120.0697 at 20iterations 2.763713 62.31302 at 30iterations 1.557224 37.77450 at 40iterations 0.8721339 17.76210 at 50iterations 0.4878590 10.96552 at 60iterations 0.2724009 6.153389 at 70iterations 0.1514834 3.576454 at 80iterations 8.4597290E-02 1.978698 at 90iterations 4.7184825E-02 1.043045 at 100iterations 2.6244273E-02 0.5589374 at 110iterations 1.4582141E-02 0.3011093 at 120iterations 8.1026144E-03 0.1703210 at 130iterations 4.5150081E-03 8.8954926E-02 at 140iterations 2.5091660E-03 5.4358721E-02 at 150iterations 1.3988968E-03 2.8514385E-02 at 160iterations 7.8022247E-04 1.5556335E-02 at 170iterations 4.3366358E-04 8.8720322E-03 at 180iterations finished qdiffx linear iterations at : 09:20:42 total time elapsed so far: 15.17000 # loops : 180 mean,max change (kT/e) : 4.3366358E-04 8.8720322E-03 energy calculations done at 15.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.35000 DelPhi exited at 09:20:43 15.350u 0.307s 0:15.93 98.2% 0+0k 0+0io 0pf+0w