Mon Oct 10 14:01:32 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 Mon Oct 10 2011 at 14:01:32 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 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: 0.5844593 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): 50.13600 111.0470 ymin,ymax (A): -18.87000 40.84000 zmin,zma (A): -34.47900 24.47900 x,y,z range (A): 60.91100 59.71000 58.95800 scale (grids/A): 0.5844593 object centre (A): 80.59150 10.98500 -5.000000 number of atom coordinates read : 3253 total number of charged atoms : 3111 net assigned charge : 5.500040 assigned positive charge : 487.1617 centred at (gu) : 88.21337 89.84547 91.46637 assigned negative charge : -481.6629 centred at (gu) : 88.15714 90.01424 91.42266 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7440 nv = 96 ne = 84 npr = 65061 no. pairs analyzed = 65061 no. exposed pairs = 4321 no. arc points = 30274 no. surface atoms = 1424 nbur = 1829 mkacc time = 0.1400000 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 = 1.456000 m= 384 mr = 3831 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3500000 number of dielectric boundary points 3971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3038 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9442 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5549684E-10 3.6496712E-09 midg,1,midg; midg,igrid,midg 6.1622698E-09 -3.2035361E-09 1,midg,midg; igrid,midg,midg -2.8004665E-10 1.9507418E-09 gauss-seidel spectral radius is 0.9849194 estimated iterations to convergence 67 setup time was (sec) 0.6000000 now iterating at: 14:01:33 rms-change max change #iterations 0.1086695 15.27523 at 10iterations 9.3160104E-03 1.202709 at 20iterations 1.2195158E-03 0.1671982 at 30iterations 3.0527185E-04 4.5352936E-02 at 40iterations 8.7582055E-05 1.3107300E-02 at 50iterations finished qdiffx linear iterations at : 14:01:35 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 8.7582055E-05 1.3107300E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 14:01:36 3.563u 0.197s 0:04.69 79.9% 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 Mon Oct 10 2011 at 14:01:37 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 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: 1.753378 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): 50.13600 111.0470 ymin,ymax (A): -18.87000 40.84000 zmin,zma (A): -34.47900 24.47900 x,y,z range (A): 60.91100 59.71000 58.95800 scale (grids/A): 1.753378 object centre (A): 80.59150 10.98500 -5.000000 number of atom coordinates read : 3253 total number of charged atoms : 3111 net assigned charge : 5.500040 assigned positive charge : 487.1617 centred at (gu) : 84.63904 89.53569 94.39806 assigned negative charge : -481.6629 centred at (gu) : 84.47097 90.04244 94.26752 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 81413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30274 grid for indexing accessible points = 1.400000 m= 28344 mr = 54827 m= 3985 mr = 19956 m= 138 mr = 2330 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 247 time to turn everything in is 0.6600000 number of dielectric boundary points 36737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 24217 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) : 0.5844593 object centre at (A) : 80.59150 10.98500 -5.000000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0349613E-02 3.0244747E-02 midg,1,midg; midg,igrid,midg 2.0063739E-02 -2.5055107E-02 1,midg,midg; igrid,midg,midg 1.3902900E-03 5.5072377E-03 gauss-seidel spectral radius is 0.9984658 estimated iterations to convergence 203 setup time was (sec) 0.9700000 now iterating at: 14:01:38 rms-change max change #iterations 4.104353 159.4035 at 10iterations 1.827518 58.58894 at 20iterations 0.8160446 29.38077 at 30iterations 0.3640157 12.62337 at 40iterations 0.1630517 4.939208 at 50iterations 7.3204070E-02 2.132597 at 60iterations 3.2835308E-02 1.139179 at 70iterations 1.4762363E-02 0.4685535 at 80iterations 6.7184330E-03 0.2073898 at 90iterations 3.0907919E-03 9.8972321E-02 at 100iterations 1.4614125E-03 5.1860809E-02 at 110iterations 7.1993569E-04 2.4116516E-02 at 120iterations finished qdiffx linear iterations at : 14:01:44 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 7.1993569E-04 2.4116516E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 14:01:45 7.866u 0.221s 0:08.92 90.5% 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 Mon Oct 10 2011 at 14:01:46 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 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: 2.630067 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): 50.13600 111.0470 ymin,ymax (A): -18.87000 40.84000 zmin,zma (A): -34.47900 24.47900 x,y,z range (A): 60.91100 59.71000 58.95800 scale (grids/A): 2.630067 object centre (A): 80.59150 10.98500 -5.000000 number of atom coordinates read : 3253 total number of charged atoms : 3111 net assigned charge : 5.500040 assigned positive charge : 487.1617 centred at (gu) : 81.95834 89.30343 96.59680 assigned negative charge : -481.6629 centred at (gu) : 81.70656 90.06352 96.40129 start vw surface at 0.1900000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 188633 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30274 grid for indexing accessible points = 1.400000 m= 92347 mr = 134042 m= 31971 mr = 73379 m= 6957 mr = 24997 m= 673 mr = 5015 m= 21 mr = 350 m= 0 mr = 12 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 866 time to turn everything in is 1.520000 number of dielectric boundary points 82807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 24880 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) : 1.753378 object centre at (A) : 80.59150 10.98500 -5.000000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1396503 0.2341705 midg,1,midg; midg,igrid,midg 0.2660742 -0.3204762 1,midg,midg; igrid,midg,midg 0.3349995 -2.5013641E-03 gauss-seidel spectral radius is 0.9992318 estimated iterations to convergence 285 setup time was (sec) 1.840000 now iterating at: 14:01:48 rms-change max change #iterations 10.19453 317.5114 at 10iterations 6.007857 170.7773 at 20iterations 3.501274 83.18816 at 30iterations 2.034849 42.99248 at 40iterations 1.175346 22.70557 at 50iterations 0.6789979 14.68500 at 60iterations 0.3888959 8.491179 at 70iterations 0.2233476 3.994204 at 80iterations 0.1278647 2.966034 at 90iterations 7.3126860E-02 1.489670 at 100iterations 4.1722078E-02 0.8123474 at 110iterations 2.3842378E-02 0.4683762 at 120iterations 1.3613666E-02 0.2474556 at 130iterations 7.7667343E-03 0.1365004 at 140iterations 4.4558761E-03 9.3040466E-02 at 150iterations 2.5588206E-03 5.1410675E-02 at 160iterations 1.4744507E-03 2.9464722E-02 at 170iterations 8.5710199E-04 1.5314102E-02 at 180iterations finished qdiffx linear iterations at : 14:01:59 total time elapsed so far: 13.58000 # loops : 180 mean,max change (kT/e) : 8.5710199E-04 1.5314102E-02 energy calculations done at 13.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 14:02:00 13.741u 0.270s 0:14.57 96.1% 0+0k 0+0io 0pf+0w