Sun Oct 9 17:08:28 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 Sun Oct 9 2011 at 17:08:28 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5276 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5461882 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): 3.273000 67.73300 ymin,ymax (A): -8.563000 54.56800 zmin,zma (A): -2.179000 63.00000 x,y,z range (A): 64.46000 63.13100 65.17900 scale (grids/A): 0.5461882 object centre (A): 35.50300 23.00250 30.41050 number of atom coordinates read : 5276 total number of charged atoms : 5141 net assigned charge : 0.6210479 assigned positive charge : 812.1462 centred at (gu) : 88.17280 88.83431 89.36233 assigned negative charge : -811.5314 centred at (gu) : 88.05693 88.89180 89.30785 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 10069 nv = 96 ne = 84 npr = 107852 no. pairs analyzed = 107852 no. exposed pairs = 6083 no. arc points = 41554 no. surface atoms = 2073 nbur = 3203 mkacc time = 0.2600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 390 mr = 5669 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 4778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4186 ## 483 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 13356 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0763312E-10 6.1503830E-10 midg,1,midg; midg,igrid,midg 1.0169232E-09 -4.7706994E-10 1,midg,midg; igrid,midg,midg -2.1735183E-09 9.2151103E-10 gauss-seidel spectral radius is 0.9828800 estimated iterations to convergence 63 setup time was (sec) 0.7700000 now iterating at: 17:08:29 rms-change max change #iterations 0.1045196 14.04525 at 10iterations 9.3180863E-03 1.438148 at 20iterations 2.6271672E-03 0.2862206 at 30iterations 1.1570624E-03 0.1210527 at 40iterations 5.2724627E-04 5.7042122E-02 at 50iterations finished qdiffx linear iterations at : 17:08:32 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 5.2724627E-04 5.7042122E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 17:08:32 3.562u 0.162s 0:04.01 92.7% 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 Sun Oct 9 2011 at 17:08:32 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5276 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.638565 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): 3.273000 67.73300 ymin,ymax (A): -8.563000 54.56800 zmin,zma (A): -2.179000 63.00000 x,y,z range (A): 64.46000 63.13100 65.17900 scale (grids/A): 1.638565 object centre (A): 35.50300 23.00250 30.41050 number of atom coordinates read : 5276 total number of charged atoms : 5141 net assigned charge : 0.6210479 assigned positive charge : 812.1462 centred at (gu) : 84.51659 86.50134 88.08575 assigned negative charge : -811.5314 centred at (gu) : 84.17084 86.67527 87.92329 start vw surface at 0.2300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 113698 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41554 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 37110 mr = 82434 m= 4033 mr = 26361 m= 117 mr = 1926 m= 0 mr = 10 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 221 time to turn everything in is 0.8200000 number of dielectric boundary points 44227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 412 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 39408 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) : 0.5461882 object centre at (A) : 35.50300 23.00250 30.41050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6886944E-02 -7.9866331E-03 midg,1,midg; midg,igrid,midg 2.6732093E-02 5.6634676E-03 1,midg,midg; igrid,midg,midg -1.7600726E-02 2.8057508E-03 gauss-seidel spectral radius is 0.9984002 estimated iterations to convergence 198 setup time was (sec) 1.100000 now iterating at: 17:08:33 rms-change max change #iterations 4.790701 158.5972 at 10iterations 2.105781 61.93317 at 20iterations 0.9252347 26.79130 at 30iterations 0.4091982 11.58869 at 40iterations 0.1808341 5.353821 at 50iterations 8.0240771E-02 2.282642 at 60iterations 3.5724998E-02 1.058411 at 70iterations 1.6408013E-02 0.4259644 at 80iterations 7.9056127E-03 0.2379227 at 90iterations 4.2028399E-03 0.1107388 at 100iterations 2.5582970E-03 7.0983887E-02 at 110iterations 1.7452680E-03 4.1589737E-02 at 120iterations finished qdiffx linear iterations at : 17:08:40 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.7452680E-03 4.1589737E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 17:08:40 7.831u 0.187s 0:08.29 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 Sun Oct 9 2011 at 17:08:40 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5276 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.457847 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): 3.273000 67.73300 ymin,ymax (A): -8.563000 54.56800 zmin,zma (A): -2.179000 63.00000 x,y,z range (A): 64.46000 63.13100 65.17900 scale (grids/A): 2.457847 object centre (A): 35.50300 23.00250 30.41050 number of atom coordinates read : 5276 total number of charged atoms : 5141 net assigned charge : 0.6210479 assigned positive charge : 812.1462 centred at (gu) : 81.77457 84.75135 87.12804 assigned negative charge : -811.5314 centred at (gu) : 81.25595 85.01298 86.88507 start vw surface at 0.2300000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 264418 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41554 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 128112 mr = 200380 m= 37840 mr = 104016 m= 6478 mr = 28699 m= 497 mr = 4126 m= 12 mr = 217 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 719 time to turn everything in is 1.990000 number of dielectric boundary points 99919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 41067 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) : 1.638565 object centre at (A) : 35.50300 23.00250 30.41050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4023122 -0.2302893 midg,1,midg; midg,igrid,midg 0.3003787 2.2815013E-02 1,midg,midg; igrid,midg,midg -0.4010763 2.1337708E-02 gauss-seidel spectral radius is 0.9992442 estimated iterations to convergence 287 setup time was (sec) 2.300000 now iterating at: 17:08:43 rms-change max change #iterations 12.20648 302.3964 at 10iterations 7.168255 193.2060 at 20iterations 4.181986 84.76099 at 30iterations 2.431217 45.57447 at 40iterations 1.406312 26.89777 at 50iterations 0.8123514 14.14248 at 60iterations 0.4674867 9.550135 at 70iterations 0.2689996 4.429959 at 80iterations 0.1547647 2.689892 at 90iterations 8.9003980E-02 1.527412 at 100iterations 5.1150441E-02 0.8314590 at 110iterations 2.9609088E-02 0.4993057 at 120iterations 1.7253784E-02 0.2946320 at 130iterations 1.0243275E-02 0.1574430 at 140iterations 6.2581813E-03 0.1072540 at 150iterations 4.0208302E-03 6.7621231E-02 at 160iterations 2.7642730E-03 4.5059204E-02 at 170iterations 2.0364956E-03 3.2184601E-02 at 180iterations finished qdiffx linear iterations at : 17:08:53 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 2.0364956E-03 3.2184601E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 17:08:54 13.022u 0.181s 0:13.48 97.9% 0+0k 0+0io 0pf+0w