Sun Oct 9 07:12:16 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 Sun Oct 9 2011 at 07:12:16 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6448224 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): -13.20100 38.48100 ymin,ymax (A): -22.20900 29.95500 zmin,zma (A): -15.64200 39.56700 x,y,z range (A): 51.68200 52.16400 55.20900 scale (grids/A): 0.6448224 object centre (A): 12.64000 3.873000 11.96250 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.1051 centred at (gu) : 90.52842 90.13598 89.25092 assigned negative charge : -298.1052 centred at (gu) : 90.67802 90.04545 89.11352 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5560 nv = 96 ne = 84 npr = 41828 no. pairs analyzed = 41828 no. exposed pairs = 2490 no. arc points = 17860 no. surface atoms = 845 nbur = 1159 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 284 mr = 2956 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.2800000 number of dielectric boundary points 2852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1729 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6520 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4540541E-08 1.3370699E-08 midg,1,midg; midg,igrid,midg -7.2143580E-09 1.1363866E-08 1,midg,midg; igrid,midg,midg 1.5092105E-08 -1.5289682E-08 gauss-seidel spectral radius is 0.9874866 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 07:12:17 rms-change max change #iterations 0.1329508 21.73391 at 10iterations 1.3504574E-02 2.154922 at 20iterations 1.3064287E-03 0.2175770 at 30iterations 1.3267242E-04 2.1579742E-02 at 40iterations 1.3187847E-05 2.2411346E-03 at 50iterations finished qdiffx linear iterations at : 07:12:20 total time elapsed so far: 3.810000 # loops : 50 mean,max change (kT/e) : 1.3187847E-05 2.2411346E-03 energy calculations done at 3.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 07:12:21 3.981u 0.277s 0:04.52 94.0% 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 07:12:21 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.934467 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): -13.20100 38.48100 ymin,ymax (A): -22.20900 29.95500 zmin,zma (A): -15.64200 39.56700 x,y,z range (A): 51.68200 52.16400 55.20900 scale (grids/A): 1.934467 object centre (A): 12.64000 3.873000 11.96250 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.1051 centred at (gu) : 91.58533 90.40793 87.75297 assigned negative charge : -298.1052 centred at (gu) : 92.03419 90.13646 87.34058 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 59434 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17860 grid for indexing accessible points = 1.400000 m= 21577 mr = 40170 m= 3218 mr = 15907 m= 159 mr = 1958 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1065 time to turn everything in is 0.5500000 number of dielectric boundary points 26287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 14712 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) : 0.6448224 object centre at (A) : 12.64000 3.873000 11.96250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4310307E-02 1.1867946E-02 midg,1,midg; midg,igrid,midg 1.2118424E-02 3.7246592E-02 1,midg,midg; igrid,midg,midg 1.0007146E-02 -2.8006511E-02 gauss-seidel spectral radius is 0.9986173 estimated iterations to convergence 213 setup time was (sec) 0.8400000 now iterating at: 07:12:22 rms-change max change #iterations 3.827036 176.1394 at 10iterations 1.781260 65.72741 at 20iterations 0.8260342 31.27833 at 30iterations 0.3863040 13.23320 at 40iterations 0.1790849 6.969338 at 50iterations 8.3821617E-02 3.168964 at 60iterations 3.9072167E-02 1.324264 at 70iterations 1.8133923E-02 0.6645136 at 80iterations 8.4852036E-03 0.3118191 at 90iterations 3.9372714E-03 0.1443825 at 100iterations 1.8367743E-03 6.7736626E-02 at 110iterations 8.5256802E-04 3.0040741E-02 at 120iterations finished qdiffx linear iterations at : 07:12:30 total time elapsed so far: 9.010000 # loops : 120 mean,max change (kT/e) : 8.5256802E-04 3.0040741E-02 energy calculations done at 9.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.180000 DelPhi exited at 07:12:30 9.186u 0.297s 0:09.78 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 Sun Oct 9 2011 at 07:12:30 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.901701 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): -13.20100 38.48100 ymin,ymax (A): -22.20900 29.95500 zmin,zma (A): -15.64200 39.56700 x,y,z range (A): 51.68200 52.16400 55.20900 scale (grids/A): 2.901701 object centre (A): 12.64000 3.873000 11.96250 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.1051 centred at (gu) : 92.37802 90.61198 86.62952 assigned negative charge : -298.1052 centred at (gu) : 93.05140 90.20474 86.01070 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 137192 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17860 grid for indexing accessible points = 1.400000 m= 69215 mr = 97300 m= 24907 mr = 56593 m= 5685 mr = 19993 m= 728 mr = 4147 m= 47 mr = 489 m= 0 mr = 25 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 3814 time to turn everything in is 1.390000 number of dielectric boundary points 59227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 14931 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) : 1.934467 object centre at (A) : 12.64000 3.873000 11.96250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6232072 9.6238166E-02 midg,1,midg; midg,igrid,midg 0.1745948 0.4500490 1,midg,midg; igrid,midg,midg 0.1636395 -0.3028708 gauss-seidel spectral radius is 0.9992437 estimated iterations to convergence 287 setup time was (sec) 1.690000 now iterating at: 07:12:32 rms-change max change #iterations 8.782702 427.3747 at 10iterations 5.029134 114.2548 at 20iterations 2.874000 58.40293 at 30iterations 1.643595 31.11975 at 40iterations 0.9393211 19.96517 at 50iterations 0.5355537 11.77896 at 60iterations 0.3045963 5.935684 at 70iterations 0.1738823 3.193018 at 80iterations 9.9098600E-02 2.149429 at 90iterations 5.6473438E-02 1.153362 at 100iterations 3.2192651E-02 0.6408834 at 110iterations 1.8345647E-02 0.3655910 at 120iterations 1.0453532E-02 0.2061596 at 130iterations 5.9501459E-03 0.1276078 at 140iterations 3.3943220E-03 6.4772129E-02 at 150iterations 1.9320181E-03 3.6385059E-02 at 160iterations 1.1038950E-03 2.3983002E-02 at 170iterations 6.2750117E-04 1.2159348E-02 at 180iterations finished qdiffx linear iterations at : 07:12:46 total time elapsed so far: 14.89000 # loops : 180 mean,max change (kT/e) : 6.2750117E-04 1.2159348E-02 energy calculations done at 14.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.07000 DelPhi exited at 07:12:46 15.068u 0.323s 0:15.65 98.2% 0+0k 0+0io 0pf+0w