Mon Oct 10 13:58:37 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+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 13:58:37 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 448 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6206740 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): -31.75500 17.63600 ymin,ymax (A): -23.10000 23.50600 zmin,zma (A): -12.49300 44.86400 x,y,z range (A): 49.39100 46.60600 57.35700 scale (grids/A): 0.6206740 object centre (A): -7.059501 0.2030001 16.18550 number of atom coordinates read : 2559 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 88.52460 88.91650 89.78766 assigned negative charge : -388.6046 centred at (gu) : 88.43827 88.96111 89.65575 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6527 nv = 96 ne = 84 npr = 52572 no. pairs analyzed = 52572 no. exposed pairs = 2995 no. arc points = 21633 no. surface atoms = 1000 nbur = 1559 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 3679 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.1900000 number of dielectric boundary points 3153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2159 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8101 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9724017E-09 1.1598582E-08 midg,1,midg; midg,igrid,midg 8.0798497E-09 2.9630526E-10 1,midg,midg; igrid,midg,midg -3.6125383E-09 6.6314465E-09 gauss-seidel spectral radius is 0.9865497 estimated iterations to convergence 71 setup time was (sec) 0.3800000 now iterating at: 13:58:38 rms-change max change #iterations 0.1270081 27.43387 at 10iterations 1.1731483E-02 2.012840 at 20iterations 1.0974855E-03 0.1645856 at 30iterations 1.1011364E-04 1.7635345E-02 at 40iterations 1.2311933E-05 2.3717880E-03 at 50iterations finished qdiffx linear iterations at : 13:58:41 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.2311933E-05 2.3717880E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 13:58:41 3.337u 0.162s 0:03.81 91.6% 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 13:58:41 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 448 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.862022 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): -31.75500 17.63600 ymin,ymax (A): -23.10000 23.50600 zmin,zma (A): -12.49300 44.86400 x,y,z range (A): 49.39100 46.60600 57.35700 scale (grids/A): 1.862022 object centre (A): -7.059501 0.2030001 16.18550 number of atom coordinates read : 2559 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 85.57313 86.74888 89.36262 assigned negative charge : -388.6046 centred at (gu) : 85.31461 86.88327 88.96708 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 70592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21633 grid for indexing accessible points = 1.400000 m= 24637 mr = 49538 m= 3487 mr = 18189 m= 158 mr = 2076 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3631 time to turn everything in is 0.3300000 number of dielectric boundary points 29032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19253 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) : 0.6206740 object centre at (A) : -7.059501 0.2030001 16.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1734221E-02 2.5555708E-02 midg,1,midg; midg,igrid,midg 1.4235861E-02 1.4631426E-03 1,midg,midg; igrid,midg,midg -2.6614193E-03 2.8371723E-02 gauss-seidel spectral radius is 0.9985659 estimated iterations to convergence 209 setup time was (sec) 0.5500000 now iterating at: 13:58:42 rms-change max change #iterations 4.038141 189.0028 at 10iterations 1.865034 60.78275 at 20iterations 0.8520881 28.49237 at 30iterations 0.3919891 13.73129 at 40iterations 0.1808167 6.001499 at 50iterations 8.3224967E-02 2.845856 at 60iterations 3.8113512E-02 1.314064 at 70iterations 1.7501751E-02 0.5846415 at 80iterations 8.0696121E-03 0.2369080 at 90iterations 3.7153908E-03 0.1182671 at 100iterations 1.7094337E-03 5.4588318E-02 at 110iterations 7.8760000E-04 2.6583672E-02 at 120iterations finished qdiffx linear iterations at : 13:58:49 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 7.8760000E-04 2.6583672E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 13:58:49 7.617u 0.188s 0:08.32 93.6% 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 13:58:50 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 448 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.793033 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): -31.75500 17.63600 ymin,ymax (A): -23.10000 23.50600 zmin,zma (A): -12.49300 44.86400 x,y,z range (A): 49.39100 46.60600 57.35700 scale (grids/A): 2.793033 object centre (A): -7.059501 0.2030001 16.18550 number of atom coordinates read : 2559 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 83.35966 85.12329 89.04401 assigned negative charge : -388.6046 centred at (gu) : 82.97182 85.32484 88.45054 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 163347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21633 grid for indexing accessible points = 1.400000 m= 81381 mr = 119767 m= 27589 mr = 67049 m= 6118 mr = 22110 m= 662 mr = 4466 m= 30 mr = 387 m= 0 mr = 12 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 12085 time to turn everything in is 0.8600000 number of dielectric boundary points 65336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 19629 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) : 1.862022 object centre at (A) : -7.059501 0.2030001 16.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1025100 0.2467854 midg,1,midg; midg,igrid,midg 0.1458892 -1.0931658E-02 1,midg,midg; igrid,midg,midg -2.0600292E-03 0.3754402 gauss-seidel spectral radius is 0.9992341 estimated iterations to convergence 285 setup time was (sec) 1.090000 now iterating at: 13:58:51 rms-change max change #iterations 9.509102 402.4501 at 10iterations 5.477482 125.0374 at 20iterations 3.129738 78.48508 at 30iterations 1.787165 42.09114 at 40iterations 1.022243 21.91062 at 50iterations 0.5809159 12.44056 at 60iterations 0.3323805 8.219132 at 70iterations 0.1887199 3.669769 at 80iterations 0.1074360 2.135389 at 90iterations 6.1152939E-02 1.251871 at 100iterations 3.4849808E-02 0.7236481 at 110iterations 1.9849434E-02 0.3659986 at 120iterations 1.1296700E-02 0.2242918 at 130iterations 6.4240326E-03 0.1212387 at 140iterations 3.6712924E-03 7.2776198E-02 at 150iterations 2.0954956E-03 3.9352417E-02 at 160iterations 1.2011367E-03 2.4385452E-02 at 170iterations 6.9075800E-04 1.3427734E-02 at 180iterations finished qdiffx linear iterations at : 13:59:02 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 6.9075800E-04 1.3427734E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 13:59:03 12.202u 0.198s 0:13.43 92.2% 0+0k 0+0io 0pf+0w