Thu Jan 19 13:32:36 PST 2012 #!/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 Thu Jan 19 2012 at 13:32:40 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6864 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4370512 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): -3.559000 62.58600 ymin,ymax (A): 17.63500 94.08400 zmin,zma (A): -15.55900 65.89600 x,y,z range (A): 66.14500 76.44900 81.45499 scale (grids/A): 0.4370512 object centre (A): 29.51350 55.85950 25.16850 number of atom coordinates read : 6864 total number of charged atoms : 6695 net assigned charge : -1.884949 assigned positive charge : 1035.045 centred at (gu) : 89.00446 90.01914 88.35992 assigned negative charge : -1036.939 centred at (gu) : 88.98019 90.02604 88.34441 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7847 nv = 96 ne = 84 npr = 138238 no. pairs analyzed = 138238 no. exposed pairs = 8919 no. arc points = 60927 no. surface atoms = 3015 nbur = 3849 mkacc time = 0.2400000 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 = 1.904000 m= 223 mr = 3735 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5072 ## 976 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3383637E-12 5.6386937E-13 midg,1,midg; midg,igrid,midg 1.2340064E-13 -1.1965701E-12 1,midg,midg; igrid,midg,midg -3.8754915E-12 1.2991887E-12 gauss-seidel spectral radius is 0.9734378 estimated iterations to convergence 51 setup time was (sec) 0.6300000 now iterating at: 13:32:44 rms-change max change #iterations 3.4161363E-02 5.138884 at 10iterations 2.7189145E-03 0.4531441 at 20iterations 9.7334187E-04 0.1614704 at 30iterations 3.8452793E-04 6.2128067E-02 at 40iterations 1.5131502E-04 2.4045944E-02 at 50iterations finished qdiffx linear iterations at : 13:32:56 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 1.5131502E-04 2.4045944E-02 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 13:32:56 3.809u 0.192s 0:16.37 24.3% 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 Thu Jan 19 2012 at 13:32:58 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6864 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.311154 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): -3.559000 62.58600 ymin,ymax (A): 17.63500 94.08400 zmin,zma (A): -15.55900 65.89600 x,y,z range (A): 66.14500 76.44900 81.45499 scale (grids/A): 1.311154 object centre (A): 29.51350 55.85950 25.16850 number of atom coordinates read : 6864 total number of charged atoms : 6695 net assigned charge : -1.884949 assigned positive charge : 1035.045 centred at (gu) : 87.01109 90.05561 85.07793 assigned negative charge : -1036.939 centred at (gu) : 86.94051 90.07789 85.03326 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 91475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60927 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 21968 mr = 60400 m= 1177 mr = 13143 m= 10 mr = 292 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 454 time to turn everything in is 0.4900000 number of dielectric boundary points 40795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1001 ## 30 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 46923 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) : 0.4370512 object centre at (A) : 29.51350 55.85950 25.16850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5311510E-03 1.1796949E-03 midg,1,midg; midg,igrid,midg -2.1240371E-03 3.2852758E-03 1,midg,midg; igrid,midg,midg -9.4268430E-04 1.8621850E-03 gauss-seidel spectral radius is 0.9975144 estimated iterations to convergence 160 setup time was (sec) 0.7300000 now iterating at: 13:33:03 rms-change max change #iterations 3.217563 149.1836 at 10iterations 1.150842 38.61349 at 20iterations 0.4148831 13.62828 at 30iterations 0.1497313 5.793945 at 40iterations 5.4211624E-02 2.088265 at 50iterations 1.9758478E-02 0.6636658 at 60iterations 7.4646701E-03 0.2910042 at 70iterations 3.1223812E-03 0.1144085 at 80iterations 1.5850085E-03 5.6451797E-02 at 90iterations 9.7233872E-04 3.3714294E-02 at 100iterations 6.5412198E-04 2.1238327E-02 at 110iterations 4.5355136E-04 1.4345169E-02 at 120iterations finished qdiffx linear iterations at : 13:33:20 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 4.5355136E-04 1.4345169E-02 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 13:33:21 8.393u 0.304s 0:23.64 36.7% 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 Thu Jan 19 2012 at 13:33:21 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6864 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.966730 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): -3.559000 62.58600 ymin,ymax (A): 17.63500 94.08400 zmin,zma (A): -15.55900 65.89600 x,y,z range (A): 66.14500 76.44900 81.45499 scale (grids/A): 1.966730 object centre (A): 29.51350 55.85950 25.16850 number of atom coordinates read : 6864 total number of charged atoms : 6695 net assigned charge : -1.884949 assigned positive charge : 1035.045 centred at (gu) : 85.51621 90.08276 82.61644 assigned negative charge : -1036.939 centred at (gu) : 85.41080 90.11667 82.54955 start vw surface at 0.1700000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 214948 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60927 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 84625 mr = 151216 m= 15799 mr = 62533 m= 1226 mr = 10078 m= 30 mr = 520 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 1423 time to turn everything in is 1.110000 number of dielectric boundary points 92281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 52879 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) : 1.311154 object centre at (A) : 29.51350 55.85950 25.16850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5465426 6.8299435E-02 midg,1,midg; midg,igrid,midg -6.4570010E-02 0.1206574 1,midg,midg; igrid,midg,midg -2.9262099E-03 4.5734964E-02 gauss-seidel spectral radius is 0.9990188 estimated iterations to convergence 252 setup time was (sec) 1.350000 now iterating at: 13:33:25 rms-change max change #iterations 9.802294 280.6910 at 10iterations 5.405802 136.8395 at 20iterations 2.936612 80.78548 at 30iterations 1.588846 35.36260 at 40iterations 0.8538753 18.04629 at 50iterations 0.4583988 12.25429 at 60iterations 0.2442111 5.038458 at 70iterations 0.1304508 2.844478 at 80iterations 6.9389112E-02 1.558036 at 90iterations 3.6929626E-02 0.7520232 at 100iterations 1.9635024E-02 0.4323578 at 110iterations 1.0425270E-02 0.2414455 at 120iterations 5.5483840E-03 0.1063328 at 130iterations 2.9644505E-03 5.7957649E-02 at 140iterations 1.5940403E-03 3.4454346E-02 at 150iterations 8.7314087E-04 1.7482758E-02 at 160iterations 4.9170107E-04 1.0189056E-02 at 170iterations 2.9134550E-04 6.2389374E-03 at 180iterations finished qdiffx linear iterations at : 13:33:50 total time elapsed so far: 13.41000 # loops : 180 mean,max change (kT/e) : 2.9134550E-04 6.2389374E-03 energy calculations done at 13.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 13:33:50 13.535u 0.292s 0:28.88 47.8% 0+0k 0+0io 0pf+0w