Wed Dec 21 14:21:28 PST 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 Wed Dec 21 2011 at 14:21:31 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ASN 136 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6349432 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): -4.650000 35.63700 ymin,ymax (A): -4.342000 49.00400 zmin,zma (A): -24.45300 31.61500 x,y,z range (A): 40.28700 53.34600 56.06800 scale (grids/A): 0.6349432 object centre (A): 15.49350 22.33100 3.581000 number of atom coordinates read : 1970 total number of charged atoms : 1766 net assigned charge : -23.32802 assigned positive charge : 264.0725 centred at (gu) : 90.28880 92.29960 89.93704 assigned negative charge : -287.4003 centred at (gu) : 90.38551 92.42384 89.88513 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5386 nv = 96 ne = 84 npr = 40428 no. pairs analyzed = 40428 no. exposed pairs = 2440 no. arc points = 17153 no. surface atoms = 829 nbur = 1141 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 267 mr = 3009 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2600000 number of dielectric boundary points 2611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1607 ## 110 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3225692E-08 -2.4714335E-08 midg,1,midg; midg,igrid,midg -1.2464421E-08 -6.2628217E-08 1,midg,midg; igrid,midg,midg -2.0503805E-08 -3.8461376E-08 gauss-seidel spectral radius is 0.9870944 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 14:21:32 rms-change max change #iterations 0.1261803 21.46597 at 10iterations 1.2101297E-02 2.068260 at 20iterations 1.1683905E-03 0.1839008 at 30iterations 1.1458791E-04 1.8361330E-02 at 40iterations 1.0906496E-05 1.9245148E-03 at 50iterations finished qdiffx linear iterations at : 14:21:36 total time elapsed so far: 4.530000 # loops : 50 mean,max change (kT/e) : 1.0906496E-05 1.9245148E-03 energy calculations done at 4.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.800000 DelPhi exited at 14:21:40 4.804u 0.396s 0:09.81 52.9% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:21:41 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ASN 136 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.904830 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): -4.650000 35.63700 ymin,ymax (A): -4.342000 49.00400 zmin,zma (A): -24.45300 31.61500 x,y,z range (A): 40.28700 53.34600 56.06800 scale (grids/A): 1.904830 object centre (A): 15.49350 22.33100 3.581000 number of atom coordinates read : 1970 total number of charged atoms : 1766 net assigned charge : -23.32802 assigned positive charge : 264.0725 centred at (gu) : 90.86679 96.89905 89.81145 assigned negative charge : -287.4003 centred at (gu) : 91.15659 97.27176 89.65560 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 58528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17153 grid for indexing accessible points = 1.400000 m= 21467 mr = 40658 m= 2962 mr = 16509 m= 163 mr = 1842 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1170 time to turn everything in is 0.5000000 number of dielectric boundary points 24058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 13902 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) : 0.6349432 object centre at (A) : 15.49350 22.33100 3.581000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0150961E-05 -7.0204943E-02 midg,1,midg; midg,igrid,midg -1.4176682E-02 -8.2232170E-02 1,midg,midg; igrid,midg,midg -1.4901211E-02 -4.1680217E-02 gauss-seidel spectral radius is 0.9985575 estimated iterations to convergence 209 setup time was (sec) 0.8100000 now iterating at: 14:21:43 rms-change max change #iterations 3.568463 167.2630 at 10iterations 1.632167 57.86061 at 20iterations 0.7486938 30.21944 at 30iterations 0.3438905 12.08526 at 40iterations 0.1575352 5.617673 at 50iterations 7.2278276E-02 2.648575 at 60iterations 3.3122264E-02 1.117893 at 70iterations 1.5150624E-02 0.5357246 at 80iterations 6.9613573E-03 0.2455912 at 90iterations 3.1772070E-03 0.1149902 at 100iterations 1.4651426E-03 5.7594299E-02 at 110iterations 6.7033700E-04 2.3696899E-02 at 120iterations finished qdiffx linear iterations at : 14:21:57 total time elapsed so far: 14.70000 # loops : 120 mean,max change (kT/e) : 6.7033700E-04 2.3696899E-02 energy calculations done at 14.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.87000 DelPhi exited at 14:22:03 14.874u 0.567s 0:21.89 70.4% 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 Wed Dec 21 2011 at 14:22:04 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ASN 136 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.857245 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): -4.650000 35.63700 ymin,ymax (A): -4.342000 49.00400 zmin,zma (A): -24.45300 31.61500 x,y,z range (A): 40.28700 53.34600 56.06800 scale (grids/A): 2.857245 object centre (A): 15.49350 22.33100 3.581000 number of atom coordinates read : 1970 total number of charged atoms : 1766 net assigned charge : -23.32802 assigned positive charge : 264.0725 centred at (gu) : 91.30029 100.3487 89.71734 assigned negative charge : -287.4003 centred at (gu) : 91.73499 100.9077 89.48343 start vw surface at 0.1100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 135241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17153 grid for indexing accessible points = 1.400000 m= 69802 mr = 98154 m= 24872 mr = 58356 m= 5080 mr = 20554 m= 634 mr = 3844 m= 38 mr = 439 m= 0 mr = 17 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 3795 time to turn everything in is 1.530000 number of dielectric boundary points 54303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 14128 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) : 1.904830 object centre at (A) : 15.49350 22.33100 3.581000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7767203 -0.7524131 midg,1,midg; midg,igrid,midg -1.8586833E-02 -0.8736981 1,midg,midg; igrid,midg,midg -0.1376070 -0.4116488 gauss-seidel spectral radius is 0.9992223 estimated iterations to convergence 283 setup time was (sec) 2.110000 now iterating at: 14:22:08 rms-change max change #iterations 8.281072 402.3103 at 10iterations 4.725049 117.5369 at 20iterations 2.664432 62.25388 at 30iterations 1.506141 32.44423 at 40iterations 0.8520019 17.02240 at 50iterations 0.4819959 9.354004 at 60iterations 0.2717132 5.641556 at 70iterations 0.1539461 3.191519 at 80iterations 8.7007567E-02 1.678711 at 90iterations 4.9145363E-02 1.101685 at 100iterations 2.7746126E-02 0.5578482 at 110iterations 1.5674977E-02 0.3047256 at 120iterations 8.8584358E-03 0.1766911 at 130iterations 5.0023254E-03 0.1024933 at 140iterations 2.8269496E-03 5.6266785E-02 at 150iterations 1.5987909E-03 3.4616470E-02 at 160iterations 9.0393942E-04 2.0094872E-02 at 170iterations 5.1110139E-04 1.0380268E-02 at 180iterations finished qdiffx linear iterations at : 14:22:30 total time elapsed so far: 24.53000 # loops : 180 mean,max change (kT/e) : 5.1110139E-04 1.0380268E-02 energy calculations done at 24.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.70000 DelPhi exited at 14:22:35 24.703u 0.973s 0:31.45 81.6% 0+0k 0+0io 0pf+0w