Sat Oct 8 19:59:16 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 Sat Oct 8 2011 at 19:59:16 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! 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: ZN6 622 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6197879 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): -31.41300 17.40200 ymin,ymax (A): -23.61500 22.72900 zmin,zma (A): -12.37300 45.06600 x,y,z range (A): 48.81500 46.34400 57.43900 scale (grids/A): 0.6197879 object centre (A): -7.005500 -0.4429998 16.34650 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.53735 89.25476 89.56456 assigned negative charge : -388.8955 centred at (gu) : 88.42944 89.31370 89.44689 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6389 nv = 96 ne = 84 npr = 54606 no. pairs analyzed = 54606 no. exposed pairs = 2978 no. arc points = 21548 no. surface atoms = 999 nbur = 1596 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 298 mr = 3535 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 0.2900000 number of dielectric boundary points 3119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2193 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8049 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5942894E-09 1.0343420E-08 midg,1,midg; midg,igrid,midg 8.9365253E-09 -1.3649147E-10 1,midg,midg; igrid,midg,midg -4.9454147E-09 7.8123419E-09 gauss-seidel spectral radius is 0.9865126 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 19:59:17 rms-change max change #iterations 0.1262137 19.68545 at 10iterations 1.1517945E-02 1.914749 at 20iterations 1.0739807E-03 0.1379986 at 30iterations 1.0004266E-04 1.3374329E-02 at 40iterations 9.2653590E-06 1.3151169E-03 at 50iterations finished qdiffx linear iterations at : 19:59:19 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 9.2653590E-06 1.3151169E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 19:59:20 3.309u 0.208s 0:03.79 92.3% 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 Sat Oct 8 2011 at 19:59:20 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! 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: ZN6 622 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.859364 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): -31.41300 17.40200 ymin,ymax (A): -23.61500 22.72900 zmin,zma (A): -12.37300 45.06600 x,y,z range (A): 48.81500 46.34400 57.43900 scale (grids/A): 1.859364 object centre (A): -7.005500 -0.4429998 16.34650 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.61166 87.76384 88.69306 assigned negative charge : -388.8955 centred at (gu) : 85.28822 87.94104 88.34053 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69997 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21548 grid for indexing accessible points = 1.400000 m= 23712 mr = 48826 m= 3343 mr = 17371 m= 162 mr = 2101 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 4024 time to turn everything in is 0.4900000 number of dielectric boundary points 28856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19353 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) : 0.6197879 object centre at (A) : -7.005500 -0.4429998 16.34650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4883464E-02 2.9084448E-02 midg,1,midg; midg,igrid,midg 1.2698962E-02 3.1933823E-04 1,midg,midg; igrid,midg,midg -5.1377498E-04 3.4967404E-02 gauss-seidel spectral radius is 0.9985634 estimated iterations to convergence 209 setup time was (sec) 0.7900000 now iterating at: 19:59:21 rms-change max change #iterations 4.007416 184.6358 at 10iterations 1.838943 61.39256 at 20iterations 0.8434088 28.10550 at 30iterations 0.3861837 11.90114 at 40iterations 0.1782190 6.574989 at 50iterations 8.1832021E-02 2.644882 at 60iterations 3.7652049E-02 1.329000 at 70iterations 1.7278422E-02 0.6297150 at 80iterations 7.9480782E-03 0.2570496 at 90iterations 3.6523067E-03 0.1232738 at 100iterations 1.6763849E-03 5.1765442E-02 at 110iterations 7.7110325E-04 2.5501251E-02 at 120iterations finished qdiffx linear iterations at : 19:59:27 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 7.7110325E-04 2.5501251E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 19:59:28 7.520u 0.230s 0:08.11 95.5% 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 19:59:28 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! 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: ZN6 622 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.789046 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): -31.41300 17.40200 ymin,ymax (A): -23.61500 22.72900 zmin,zma (A): -12.37300 45.06600 x,y,z range (A): 48.81500 46.34400 57.43900 scale (grids/A): 2.789046 object centre (A): -7.005500 -0.4429998 16.34650 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.41728 86.64574 88.03957 assigned negative charge : -388.8955 centred at (gu) : 82.93224 86.91154 87.51078 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 162015 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21548 grid for indexing accessible points = 1.400000 m= 78915 mr = 118165 m= 26471 mr = 64786 m= 5919 mr = 21154 m= 751 mr = 4447 m= 36 mr = 508 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 14416 time to turn everything in is 1.210000 number of dielectric boundary points 65034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 19727 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) : 1.859364 object centre at (A) : -7.005500 -0.4429998 16.34650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7673765E-02 0.3794840 midg,1,midg; midg,igrid,midg 0.1508956 -7.8288196E-03 1,midg,midg; igrid,midg,midg -2.6354367E-02 0.4656538 gauss-seidel spectral radius is 0.9992323 estimated iterations to convergence 285 setup time was (sec) 1.520000 now iterating at: 19:59:30 rms-change max change #iterations 9.429928 305.3036 at 10iterations 5.413012 119.4028 at 20iterations 3.088819 75.81795 at 30iterations 1.759528 34.60564 at 40iterations 1.001861 23.16128 at 50iterations 0.5707207 11.32199 at 60iterations 0.3249234 7.289251 at 70iterations 0.1846050 3.608154 at 80iterations 0.1049955 2.060770 at 90iterations 5.9757303E-02 1.155588 at 100iterations 3.3991497E-02 0.7541232 at 110iterations 1.9310636E-02 0.3647385 at 120iterations 1.0990473E-02 0.2199068 at 130iterations 6.2298011E-03 0.1251020 at 140iterations 3.5443569E-03 7.3665619E-02 at 150iterations 2.0180959E-03 3.6003113E-02 at 160iterations 1.1461226E-03 2.1302223E-02 at 170iterations 6.5192883E-04 1.2357712E-02 at 180iterations finished qdiffx linear iterations at : 19:59:40 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 6.5192883E-04 1.2357712E-02 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 19:59:41 12.191u 0.240s 0:12.75 97.4% 0+0k 0+0io 0pf+0w