Tue Oct 11 03:43:52 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 Tue Oct 11 2011 at 03:43:52 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 = 2774 !!! WARNING: ASP 288 has a net charge of -0.7280 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: 0.6314408 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): 10.42400 65.17000 ymin,ymax (A): -5.593000 47.23400 zmin,zma (A): -9.806001 46.57300 x,y,z range (A): 54.74600 52.82700 56.37900 scale (grids/A): 0.6314408 object centre (A): 37.79700 20.82050 18.38350 number of atom coordinates read : 2774 total number of charged atoms : 2625 net assigned charge : 4.772016 assigned positive charge : 420.6387 centred at (gu) : 91.75294 90.33090 91.32614 assigned negative charge : -415.8673 centred at (gu) : 91.50595 90.51884 91.38556 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7364 nv = 96 ne = 84 npr = 56257 no. pairs analyzed = 56257 no. exposed pairs = 3356 no. arc points = 23930 no. surface atoms = 1123 nbur = 1651 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 4056 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2428 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2272553E-09 -1.1300280E-09 midg,1,midg; midg,igrid,midg 2.1589711E-08 -1.4796747E-08 1,midg,midg; igrid,midg,midg -1.3422635E-08 4.2311477E-08 gauss-seidel spectral radius is 0.9870223 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 03:43:52 rms-change max change #iterations 0.1387122 19.28114 at 10iterations 1.3302493E-02 2.269929 at 20iterations 1.2885635E-03 0.1870785 at 30iterations 1.2645373E-04 1.7850876E-02 at 40iterations 1.2957196E-05 1.7127991E-03 at 50iterations finished qdiffx linear iterations at : 03:43:55 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.2957196E-05 1.7127991E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 03:43:56 3.363u 0.132s 0:04.04 86.3% 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 Tue Oct 11 2011 at 03:43:56 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 = 2774 !!! WARNING: ASP 288 has a net charge of -0.7280 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: 1.894322 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): 10.42400 65.17000 ymin,ymax (A): -5.593000 47.23400 zmin,zma (A): -9.806001 46.57300 x,y,z range (A): 54.74600 52.82700 56.37900 scale (grids/A): 1.894322 object centre (A): 37.79700 20.82050 18.38350 number of atom coordinates read : 2774 total number of charged atoms : 2625 net assigned charge : 4.772016 assigned positive charge : 420.6387 centred at (gu) : 95.25850 90.99233 93.97758 assigned negative charge : -415.8673 centred at (gu) : 94.51759 91.55637 94.15648 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23930 grid for indexing accessible points = 1.400000 m= 29371 mr = 54681 m= 4613 mr = 21959 m= 314 mr = 3012 m= 0 mr = 119 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 309 time to turn everything in is 0.5900000 number of dielectric boundary points 33413 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20636 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) : 0.6314408 object centre at (A) : 37.79700 20.82050 18.38350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2410190E-02 -2.2902319E-02 midg,1,midg; midg,igrid,midg 2.5946356E-02 -6.0619516E-03 1,midg,midg; igrid,midg,midg -5.1908698E-03 6.9196634E-02 gauss-seidel spectral radius is 0.9986387 estimated iterations to convergence 215 setup time was (sec) 0.8700000 now iterating at: 03:43:57 rms-change max change #iterations 4.324366 197.6423 at 10iterations 2.029127 69.56674 at 20iterations 0.9496199 30.22536 at 30iterations 0.4453180 13.76821 at 40iterations 0.2099324 7.212461 at 50iterations 9.7967193E-02 3.369118 at 60iterations 4.6123430E-02 1.358170 at 70iterations 2.1555848E-02 0.6648331 at 80iterations 1.0127135E-02 0.3196363 at 90iterations 4.7525866E-03 0.1377716 at 100iterations 2.2394056E-03 6.5629959E-02 at 110iterations 1.0484386E-03 3.0284882E-02 at 120iterations finished qdiffx linear iterations at : 03:44:03 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 1.0484386E-03 3.0284882E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 03:44:04 7.630u 0.198s 0:08.26 94.6% 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 Tue Oct 11 2011 at 03:44:04 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 = 2774 !!! WARNING: ASP 288 has a net charge of -0.7280 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: 2.841484 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): 10.42400 65.17000 ymin,ymax (A): -5.593000 47.23400 zmin,zma (A): -9.806001 46.57300 x,y,z range (A): 54.74600 52.82700 56.37900 scale (grids/A): 2.841484 object centre (A): 37.79700 20.82050 18.38350 number of atom coordinates read : 2774 total number of charged atoms : 2625 net assigned charge : 4.772016 assigned positive charge : 420.6387 centred at (gu) : 97.88762 91.48837 95.96624 assigned negative charge : -415.8673 centred at (gu) : 96.77637 92.33449 96.23461 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 182294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23930 grid for indexing accessible points = 1.400000 m= 94160 mr = 132416 m= 34704 mr = 77518 m= 8323 mr = 28316 m= 1268 mr = 6416 m= 103 mr = 877 m= 0 mr = 41 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 1139 time to turn everything in is 1.500000 number of dielectric boundary points 75268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 21000 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) : 1.894322 object centre at (A) : 37.79700 20.82050 18.38350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2834552 -0.4559431 midg,1,midg; midg,igrid,midg 0.2830657 0.1022868 1,midg,midg; igrid,midg,midg -4.3203630E-02 0.6666553 gauss-seidel spectral radius is 0.9992623 estimated iterations to convergence 291 setup time was (sec) 1.820000 now iterating at: 03:44:06 rms-change max change #iterations 10.24789 522.9785 at 10iterations 6.020076 140.0807 at 20iterations 3.522035 82.78323 at 30iterations 2.046348 40.32701 at 40iterations 1.186812 23.41220 at 50iterations 0.6874900 12.73077 at 60iterations 0.3978412 7.360565 at 70iterations 0.2301264 4.402592 at 80iterations 0.1326371 2.316938 at 90iterations 7.6541744E-02 1.346495 at 100iterations 4.4067074E-02 0.7837172 at 110iterations 2.5404392E-02 0.4431024 at 120iterations 1.4641888E-02 0.2719765 at 130iterations 8.4425276E-03 0.1488105 at 140iterations 4.8541524E-03 8.9501858E-02 at 150iterations 2.7929309E-03 4.9541950E-02 at 160iterations 1.6115785E-03 2.8182983E-02 at 170iterations 9.2969235E-04 1.6397476E-02 at 180iterations finished qdiffx linear iterations at : 03:44:17 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 9.2969235E-04 1.6397476E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 03:44:17 12.534u 0.197s 0:13.09 97.1% 0+0k 0+0io 0pf+0w