Mon Oct 10 23:52:37 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 Mon Oct 10 2011 at 23:52:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2662 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: 0.6314072 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): 18.02300 74.34600 ymin,ymax (A): -11.51200 44.87000 zmin,zma (A): -7.709000 35.10800 x,y,z range (A): 56.32300 56.38200 42.81700 scale (grids/A): 0.6314072 object centre (A): 46.18450 16.67900 13.69950 number of atom coordinates read : 2662 total number of charged atoms : 2518 net assigned charge : 2.500015 assigned positive charge : 399.8387 centred at (gu) : 88.56157 89.37946 89.84032 assigned negative charge : -397.3394 centred at (gu) : 88.78423 89.53439 90.03228 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7035 nv = 96 ne = 84 npr = 54683 no. pairs analyzed = 54683 no. exposed pairs = 3104 no. arc points = 21802 no. surface atoms = 1055 nbur = 1607 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 4044 m= 0 mr = 64 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.4100000 number of dielectric boundary points 3291 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2105 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 8570 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0810765E-08 -1.5473766E-08 midg,1,midg; midg,igrid,midg 1.9185238E-08 -1.0809442E-08 1,midg,midg; igrid,midg,midg 3.1416704E-08 -1.3866434E-08 gauss-seidel spectral radius is 0.9870076 estimated iterations to convergence 72 setup time was (sec) 0.7600000 now iterating at: 23:52:38 rms-change max change #iterations 0.1347447 19.68293 at 10iterations 1.3852197E-02 2.101349 at 20iterations 1.8504361E-03 0.3427849 at 30iterations 4.5924250E-04 9.9430084E-02 at 40iterations 1.3485755E-04 3.0872345E-02 at 50iterations finished qdiffx linear iterations at : 23:52:42 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 1.3485755E-04 3.0872345E-02 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 23:52:43 4.538u 0.391s 0:05.38 91.4% 0+0k 0+0io 5pf+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 23:52:43 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 = 2662 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: 1.894222 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): 18.02300 74.34600 ymin,ymax (A): -11.51200 44.87000 zmin,zma (A): -7.709000 35.10800 x,y,z range (A): 56.32300 56.38200 42.81700 scale (grids/A): 1.894222 object centre (A): 46.18450 16.67900 13.69950 number of atom coordinates read : 2662 total number of charged atoms : 2518 net assigned charge : 2.500015 assigned positive charge : 399.8387 centred at (gu) : 85.68391 88.13775 89.52016 assigned negative charge : -397.3394 centred at (gu) : 86.35229 88.60278 90.09647 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 76866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21802 grid for indexing accessible points = 1.400000 m= 27127 mr = 54647 m= 4104 mr = 20421 m= 211 mr = 2679 m= 0 mr = 66 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1350 time to turn everything in is 0.7700000 number of dielectric boundary points 30495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 19824 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) : 0.6314072 object centre at (A) : 46.18450 16.67900 13.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5493765E-02 2.0368411E-03 midg,1,midg; midg,igrid,midg 4.9710166E-02 -2.9720660E-02 1,midg,midg; igrid,midg,midg -2.1810478E-02 -6.8659052E-02 gauss-seidel spectral radius is 0.9986198 estimated iterations to convergence 213 setup time was (sec) 1.090000 now iterating at: 23:52:44 rms-change max change #iterations 4.254879 200.9100 at 10iterations 1.978974 73.59731 at 20iterations 0.9226136 29.21778 at 30iterations 0.4294772 15.09025 at 40iterations 0.2019066 6.724861 at 50iterations 9.4086982E-02 3.077533 at 60iterations 4.3955307E-02 1.320092 at 70iterations 2.0763982E-02 0.6253357 at 80iterations 9.8188827E-03 0.3687401 at 90iterations 4.7399243E-03 0.1536179 at 100iterations 2.3648005E-03 9.1794074E-02 at 110iterations 1.2444949E-03 4.6424866E-02 at 120iterations finished qdiffx linear iterations at : 23:52:53 total time elapsed so far: 10.05000 # loops : 120 mean,max change (kT/e) : 1.2444949E-03 4.6424866E-02 energy calculations done at 10.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.26000 DelPhi exited at 23:52:54 10.261u 0.449s 0:11.07 96.6% 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 Mon Oct 10 2011 at 23:52:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2662 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: 2.841332 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): 18.02300 74.34600 ymin,ymax (A): -11.51200 44.87000 zmin,zma (A): -7.709000 35.10800 x,y,z range (A): 56.32300 56.38200 42.81700 scale (grids/A): 2.841332 object centre (A): 46.18450 16.67900 13.69950 number of atom coordinates read : 2662 total number of charged atoms : 2518 net assigned charge : 2.500015 assigned positive charge : 399.8387 centred at (gu) : 83.52580 87.20646 89.28003 assigned negative charge : -397.3394 centred at (gu) : 84.52843 87.90418 90.14461 start vw surface at 0.1600000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 178124 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21802 grid for indexing accessible points = 1.400000 m= 89699 mr = 132513 m= 31503 mr = 74352 m= 7376 mr = 25688 m= 927 mr = 5676 m= 38 mr = 607 m= 0 mr = 19 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 4592 time to turn everything in is 2.010000 number of dielectric boundary points 68812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 20140 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) : 1.894222 object centre at (A) : 46.18450 16.67900 13.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3640616 6.3033752E-02 midg,1,midg; midg,igrid,midg 0.6850829 -0.5017724 1,midg,midg; igrid,midg,midg -0.2146582 -0.7657546 gauss-seidel spectral radius is 0.9992509 estimated iterations to convergence 288 setup time was (sec) 2.350000 now iterating at: 23:52:57 rms-change max change #iterations 9.929370 472.6949 at 10iterations 5.735919 110.1845 at 20iterations 3.296121 66.89847 at 30iterations 1.894860 34.37928 at 40iterations 1.087421 21.10470 at 50iterations 0.6217838 11.28952 at 60iterations 0.3568964 7.161061 at 70iterations 0.2047080 4.072556 at 80iterations 0.1173143 2.174175 at 90iterations 6.7200251E-02 1.184204 at 100iterations 3.8561348E-02 0.7031822 at 110iterations 2.2189086E-02 0.4386597 at 120iterations 1.2830937E-02 0.2437325 at 130iterations 7.4685132E-03 0.1394043 at 140iterations 4.4164974E-03 8.6582184E-02 at 150iterations 2.6759910E-03 6.3322544E-02 at 160iterations 1.6940194E-03 3.8841248E-02 at 170iterations 1.1326316E-03 2.6519775E-02 at 180iterations finished qdiffx linear iterations at : 23:53:11 total time elapsed so far: 17.29000 # loops : 180 mean,max change (kT/e) : 1.1326316E-03 2.6519775E-02 energy calculations done at 17.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.49000 DelPhi exited at 23:53:12 17.498u 0.501s 0:18.41 97.7% 0+0k 0+0io 0pf+0w