Sat Oct 8 16:13:20 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 Sat Oct 8 2011 at 16:13:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2446 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: 0.6255491 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): -2.423000 45.00900 ymin,ymax (A): -15.38900 29.74400 zmin,zma (A): -18.69900 38.21100 x,y,z range (A): 47.43200 45.13300 56.91000 scale (grids/A): 0.6255491 object centre (A): 21.29300 7.177500 9.756001 number of atom coordinates read : 2446 total number of charged atoms : 2387 net assigned charge : 2.000003 assigned positive charge : 367.6059 centred at (gu) : 91.21543 88.64463 90.06155 assigned negative charge : -365.6068 centred at (gu) : 91.31700 88.79299 90.16823 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6496 nv = 96 ne = 84 npr = 48281 no. pairs analyzed = 48281 no. exposed pairs = 3188 no. arc points = 21726 no. surface atoms = 1086 nbur = 1360 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 355 mr = 3585 m= 0 mr = 46 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2156 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.4469241E-09 -6.1325314E-09 midg,1,midg; midg,igrid,midg 1.6962739E-08 -6.7854717E-09 1,midg,midg; igrid,midg,midg 7.0613462E-09 -7.4799322E-09 gauss-seidel spectral radius is 0.9867537 estimated iterations to convergence 71 setup time was (sec) 0.4700000 now iterating at: 16:13:21 rms-change max change #iterations 0.1265235 19.02217 at 10iterations 1.1805166E-02 1.817585 at 20iterations 1.1826674E-03 0.1822433 at 30iterations 1.5178886E-04 2.2407532E-02 at 40iterations 3.1617732E-05 4.6935081E-03 at 50iterations finished qdiffx linear iterations at : 16:13:23 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 3.1617732E-05 4.6935081E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 16:13:24 3.080u 0.162s 0:03.55 91.2% 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 Sat Oct 8 2011 at 16:13:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2446 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: 1.876647 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): -2.423000 45.00900 ymin,ymax (A): -15.38900 29.74400 zmin,zma (A): -18.69900 38.21100 x,y,z range (A): 47.43200 45.13300 56.91000 scale (grids/A): 1.876647 object centre (A): 21.29300 7.177500 9.756001 number of atom coordinates read : 2446 total number of charged atoms : 2387 net assigned charge : 2.000003 assigned positive charge : 367.6059 centred at (gu) : 93.64587 85.93345 90.18386 assigned negative charge : -365.6068 centred at (gu) : 93.95068 86.37888 90.50451 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 24459 mr = 49219 m= 3822 mr = 17645 m= 205 mr = 2405 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 228 time to turn everything in is 0.4900000 number of dielectric boundary points 29909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 18742 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) : 0.6255491 object centre at (A) : 21.29300 7.177500 9.756001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6068887E-02 -1.9961849E-02 midg,1,midg; midg,igrid,midg 2.6445227E-02 -4.4114902E-03 1,midg,midg; igrid,midg,midg 5.3611742E-03 -4.0672440E-02 gauss-seidel spectral radius is 0.9985833 estimated iterations to convergence 211 setup time was (sec) 0.7400000 now iterating at: 16:13:25 rms-change max change #iterations 4.009480 215.4106 at 10iterations 1.836492 74.63568 at 20iterations 0.8556603 28.43112 at 30iterations 0.3946831 12.16960 at 40iterations 0.1824988 6.178009 at 50iterations 8.4331483E-02 2.922050 at 60iterations 3.9004177E-02 1.353267 at 70iterations 1.8044110E-02 0.5612392 at 80iterations 8.3538499E-03 0.2792730 at 90iterations 3.8688371E-03 0.1305885 at 100iterations 1.7933372E-03 5.8686972E-02 at 110iterations 8.3536515E-04 2.5840759E-02 at 120iterations finished qdiffx linear iterations at : 16:13:31 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 8.3536515E-04 2.5840759E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 16:13:31 6.918u 0.196s 0:07.41 95.8% 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 Sat Oct 8 2011 at 16:13:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2446 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: 2.814971 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): -2.423000 45.00900 ymin,ymax (A): -15.38900 29.74400 zmin,zma (A): -18.69900 38.21100 x,y,z range (A): 47.43200 45.13300 56.91000 scale (grids/A): 2.814971 object centre (A): 21.29300 7.177500 9.756001 number of atom coordinates read : 2446 total number of charged atoms : 2387 net assigned charge : 2.000003 assigned positive charge : 367.6059 centred at (gu) : 95.46861 83.89993 90.27565 assigned negative charge : -365.6068 centred at (gu) : 95.92606 84.56829 90.75670 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 163825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 80470 mr = 119545 m= 28100 mr = 65184 m= 6875 mr = 22392 m= 905 mr = 5099 m= 45 mr = 553 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 850 time to turn everything in is 1.230000 number of dielectric boundary points 67424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19095 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) : 1.876647 object centre at (A) : 21.29300 7.177500 9.756001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1725606 -0.2623601 midg,1,midg; midg,igrid,midg 0.2448855 -5.2950218E-02 1,midg,midg; igrid,midg,midg 4.1037001E-02 -0.5216472 gauss-seidel spectral radius is 0.9992462 estimated iterations to convergence 287 setup time was (sec) 1.510000 now iterating at: 16:13:33 rms-change max change #iterations 9.557851 303.0535 at 10iterations 5.639346 133.2917 at 20iterations 3.286821 70.71499 at 30iterations 1.916130 42.76458 at 40iterations 1.108429 22.13997 at 50iterations 0.6411467 13.20075 at 60iterations 0.3694589 6.839342 at 70iterations 0.2123509 4.338530 at 80iterations 0.1223847 2.305374 at 90iterations 7.0273459E-02 1.271027 at 100iterations 4.0300570E-02 0.7080357 at 110iterations 2.3066023E-02 0.4247894 at 120iterations 1.3226637E-02 0.2464402 at 130iterations 7.5950571E-03 0.1541042 at 140iterations 4.3469002E-03 8.2653046E-02 at 150iterations 2.4949531E-03 4.5970917E-02 at 160iterations 1.4298479E-03 2.7922630E-02 at 170iterations 8.2668202E-04 1.6321182E-02 at 180iterations finished qdiffx linear iterations at : 16:13:42 total time elapsed so far: 10.96000 # loops : 180 mean,max change (kT/e) : 8.2668202E-04 1.6321182E-02 energy calculations done at 10.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.13000 DelPhi exited at 16:13:43 11.135u 0.183s 0:11.63 97.2% 0+0k 0+0io 0pf+0w