Sat Oct 8 14:20:41 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 Sat Oct 8 2011 at 14:20:41 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3023 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6399080 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): -12.03200 43.60100 ymin,ymax (A): -22.24500 22.66500 zmin,zma (A): -8.303000 46.92000 x,y,z range (A): 55.63300 44.91000 55.22300 scale (grids/A): 0.6399080 object centre (A): 15.78450 0.2099991 19.30850 number of atom coordinates read : 3023 total number of charged atoms : 2876 net assigned charge : 1.4008060E-02 assigned positive charge : 453.7186 centred at (gu) : 88.72858 89.45332 92.09508 assigned negative charge : -453.7053 centred at (gu) : 88.72608 89.36520 92.01288 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8259 nv = 96 ne = 84 npr = 63429 no. pairs analyzed = 63429 no. exposed pairs = 3456 no. arc points = 23893 no. surface atoms = 1174 nbur = 1849 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4843 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2300 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9957 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2309145E-09 1.7248508E-08 midg,1,midg; midg,igrid,midg -1.3723809E-08 1.0333974E-08 1,midg,midg; igrid,midg,midg -6.4936712E-10 1.3976099E-10 gauss-seidel spectral radius is 0.9873779 estimated iterations to convergence 73 setup time was (sec) 0.6500000 now iterating at: 14:20:42 rms-change max change #iterations 0.1593079 20.36402 at 10iterations 1.6249038E-02 2.147837 at 20iterations 1.7039177E-03 0.2254877 at 30iterations 2.1462013E-04 3.1276703E-02 at 40iterations 3.5657333E-05 5.2890778E-03 at 50iterations finished qdiffx linear iterations at : 14:20:45 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 3.5657333E-05 5.2890778E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 14:20:46 4.154u 0.290s 0:04.71 94.2% 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 14:20:46 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3023 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.919724 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): -12.03200 43.60100 ymin,ymax (A): -22.24500 22.66500 zmin,zma (A): -8.303000 46.92000 x,y,z range (A): 55.63300 44.91000 55.22300 scale (grids/A): 1.919724 object centre (A): 15.78450 0.2099991 19.30850 number of atom coordinates read : 3023 total number of charged atoms : 2876 net assigned charge : 1.4008060E-02 assigned positive charge : 453.7186 centred at (gu) : 86.18492 88.35942 96.28493 assigned negative charge : -453.7053 centred at (gu) : 86.17796 88.09526 96.03838 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 89298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23893 grid for indexing accessible points = 1.400000 m= 32914 mr = 64749 m= 5071 mr = 24766 m= 282 mr = 3113 m= 6 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 34857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 22674 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) : 0.6399080 object centre at (A) : 15.78450 0.2099991 19.30850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9612882E-02 2.8586732E-02 midg,1,midg; midg,igrid,midg -1.7977986E-04 1.7934620E-02 1,midg,midg; igrid,midg,midg -4.1749753E-02 3.9326609E-03 gauss-seidel spectral radius is 0.9986880 estimated iterations to convergence 219 setup time was (sec) 1.080000 now iterating at: 14:20:47 rms-change max change #iterations 4.712588 175.8143 at 10iterations 2.255600 67.54257 at 20iterations 1.073426 32.79364 at 30iterations 0.5114738 15.59949 at 40iterations 0.2434142 6.752210 at 50iterations 0.1160658 3.269976 at 60iterations 5.5209916E-02 1.581505 at 70iterations 2.6325230E-02 0.7656693 at 80iterations 1.2560607E-02 0.3410072 at 90iterations 5.9633343E-03 0.1698542 at 100iterations 2.8525738E-03 8.1071377E-02 at 110iterations 1.3618583E-03 3.7811279E-02 at 120iterations finished qdiffx linear iterations at : 14:20:56 total time elapsed so far: 9.620000 # loops : 120 mean,max change (kT/e) : 1.3618583E-03 3.7811279E-02 energy calculations done at 9.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.800000 DelPhi exited at 14:20:56 9.806u 0.301s 0:10.43 96.8% 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 14:20:56 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3023 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.879586 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): -12.03200 43.60100 ymin,ymax (A): -22.24500 22.66500 zmin,zma (A): -8.303000 46.92000 x,y,z range (A): 55.63300 44.91000 55.22300 scale (grids/A): 2.879586 object centre (A): 15.78450 0.2099991 19.30850 number of atom coordinates read : 3023 total number of charged atoms : 2876 net assigned charge : 1.4008060E-02 assigned positive charge : 453.7186 centred at (gu) : 84.27729 87.53897 99.42709 assigned negative charge : -453.7053 centred at (gu) : 84.26688 87.14279 99.05762 start vw surface at 0.1700000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 206933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23893 grid for indexing accessible points = 1.400000 m= 107420 mr = 156341 m= 38439 mr = 89638 m= 9185 mr = 31237 m= 1281 mr = 6815 m= 70 mr = 783 m= 0 mr = 16 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.060000 number of dielectric boundary points 78498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 23006 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) : 1.919724 object centre at (A) : 15.78450 0.2099991 19.30850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7280219E-02 0.5730147 midg,1,midg; midg,igrid,midg 1.6861213E-02 0.2060490 1,midg,midg; igrid,midg,midg -0.7390060 0.1136006 gauss-seidel spectral radius is 0.9992785 estimated iterations to convergence 294 setup time was (sec) 2.400000 now iterating at: 14:20:59 rms-change max change #iterations 11.01314 452.6565 at 10iterations 6.480842 138.6972 at 20iterations 3.782873 76.64598 at 30iterations 2.212729 42.42197 at 40iterations 1.288216 25.60303 at 50iterations 0.7506782 12.83955 at 60iterations 0.4359824 7.849731 at 70iterations 0.2532589 4.955050 at 80iterations 0.1470048 2.467850 at 90iterations 8.5248657E-02 1.462215 at 100iterations 4.9425717E-02 0.7570000 at 110iterations 2.8627593E-02 0.4861736 at 120iterations 1.6629141E-02 0.2775459 at 130iterations 9.6473396E-03 0.1723661 at 140iterations 5.6006345E-03 9.4258666E-02 at 150iterations 3.2614677E-03 5.7136387E-02 at 160iterations 1.9078340E-03 3.0218363E-02 at 170iterations 1.1204586E-03 1.7899990E-02 at 180iterations finished qdiffx linear iterations at : 14:21:13 total time elapsed so far: 16.78000 # loops : 180 mean,max change (kT/e) : 1.1204586E-03 1.7899990E-02 energy calculations done at 16.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.96000 DelPhi exited at 14:21:14 16.965u 0.323s 0:17.60 98.1% 0+0k 0+0io 0pf+0w