Sat Oct 15 13:20:14 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 15 2011 at 13:20:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 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: 0.6042604 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): -41.65200 13.12100 ymin,ymax (A): 26.80000 85.71500 zmin,zma (A): 28.65000 82.29601 x,y,z range (A): 54.77299 58.91500 53.64600 scale (grids/A): 0.6042604 object centre (A): -14.26550 56.25750 55.47300 number of atom coordinates read : 2950 total number of charged atoms : 2810 net assigned charge : 1.500005 assigned positive charge : 447.3595 centred at (gu) : 90.29939 89.66776 87.92678 assigned negative charge : -445.8604 centred at (gu) : 90.41180 89.64904 87.92963 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7227 nv = 96 ne = 84 npr = 56599 no. pairs analyzed = 56599 no. exposed pairs = 3990 no. arc points = 28996 no. surface atoms = 1315 nbur = 1635 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3595 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2100000 number of dielectric boundary points 3941 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2866 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8961 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4140012E-09 3.9808359E-10 midg,1,midg; midg,igrid,midg -1.5108559E-10 1.5256890E-09 1,midg,midg; igrid,midg,midg 5.6343223E-09 -4.9954578E-09 gauss-seidel spectral radius is 0.9858649 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 13:20:15 rms-change max change #iterations 0.1155123 17.65842 at 10iterations 9.9585177E-03 1.307037 at 20iterations 8.6663006E-04 0.1395702 at 30iterations 7.5954318E-05 1.1521816E-02 at 40iterations 7.1659188E-06 9.3317032E-04 at 50iterations finished qdiffx linear iterations at : 13:20:19 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 7.1659188E-06 9.3317032E-04 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 13:20:19 3.586u 0.186s 0:04.84 77.6% 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 Sat Oct 15 2011 at 13:20:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 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: 1.812781 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): -41.65200 13.12100 ymin,ymax (A): 26.80000 85.71500 zmin,zma (A): 28.65000 82.29601 x,y,z range (A): 54.77299 58.91500 53.64600 scale (grids/A): 1.812781 object centre (A): -14.26550 56.25750 55.47300 number of atom coordinates read : 2950 total number of charged atoms : 2810 net assigned charge : 1.500005 assigned positive charge : 447.3595 centred at (gu) : 90.89734 89.00259 83.77971 assigned negative charge : -445.8604 centred at (gu) : 91.23505 88.94691 83.78873 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78559 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28996 grid for indexing accessible points = 1.400000 m= 24247 mr = 51318 m= 3039 mr = 16553 m= 136 mr = 1656 m= 0 mr = 41 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1228 time to turn everything in is 0.3800000 number of dielectric boundary points 36413 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 21945 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) : 0.6042604 object centre at (A) : -14.26550 56.25750 55.47300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1742612E-02 -3.3617571E-03 midg,1,midg; midg,igrid,midg 2.1988178E-02 1.0876068E-02 1,midg,midg; igrid,midg,midg 1.7072482E-02 -8.2941428E-03 gauss-seidel spectral radius is 0.9985449 estimated iterations to convergence 208 setup time was (sec) 0.6300000 now iterating at: 13:20:20 rms-change max change #iterations 4.170877 172.8526 at 10iterations 1.896288 70.17149 at 20iterations 0.8665066 26.42395 at 30iterations 0.3958489 12.96783 at 40iterations 0.1812157 5.404288 at 50iterations 8.2705863E-02 2.590823 at 60iterations 3.7669741E-02 1.369934 at 70iterations 1.7192157E-02 0.5592506 at 80iterations 7.8638680E-03 0.2467232 at 90iterations 3.5948418E-03 0.1175699 at 100iterations 1.6435927E-03 5.5124283E-02 at 110iterations 7.4902805E-04 2.4247169E-02 at 120iterations finished qdiffx linear iterations at : 13:20:28 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 7.4902805E-04 2.4247169E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 13:20:28 8.183u 0.241s 0:08.81 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 15 2011 at 13:20:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 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: 2.719172 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): -41.65200 13.12100 ymin,ymax (A): 26.80000 85.71500 zmin,zma (A): 28.65000 82.29601 x,y,z range (A): 54.77299 58.91500 53.64600 scale (grids/A): 2.719172 object centre (A): -14.26550 56.25750 55.47300 number of atom coordinates read : 2950 total number of charged atoms : 2810 net assigned charge : 1.500005 assigned positive charge : 447.3595 centred at (gu) : 91.34608 88.50365 80.66946 assigned negative charge : -445.8604 centred at (gu) : 91.85249 88.42044 80.68315 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 182370 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28996 grid for indexing accessible points = 1.400000 m= 82618 mr = 126010 m= 25025 mr = 64674 m= 4976 mr = 18999 m= 607 mr = 3464 m= 26 mr = 361 m= 0 mr = 4 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 4138 time to turn everything in is 0.9400000 number of dielectric boundary points 82110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 22478 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) : 1.812781 object centre at (A) : -14.26550 56.25750 55.47300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1219375 -5.6099579E-02 midg,1,midg; midg,igrid,midg 0.3528370 8.2488000E-02 1,midg,midg; igrid,midg,midg 0.1737632 2.7113797E-02 gauss-seidel spectral radius is 0.9992520 estimated iterations to convergence 289 setup time was (sec) 1.200000 now iterating at: 13:20:30 rms-change max change #iterations 10.03464 297.4928 at 10iterations 5.884636 157.0529 at 20iterations 3.429593 90.40817 at 30iterations 1.985019 52.39703 at 40iterations 1.150497 29.60588 at 50iterations 0.6642751 14.50750 at 60iterations 0.3821687 8.264798 at 70iterations 0.2202440 4.977301 at 80iterations 0.1263835 2.690890 at 90iterations 7.2618008E-02 1.492938 at 100iterations 4.1630901E-02 0.9228649 at 110iterations 2.3918066E-02 0.5345230 at 120iterations 1.3666647E-02 0.2626425 at 130iterations 7.8307213E-03 0.1460457 at 140iterations 4.4937967E-03 8.7484360E-02 at 150iterations 2.5787186E-03 4.8967361E-02 at 160iterations 1.4761332E-03 2.8961182E-02 at 170iterations 8.4568153E-04 1.6485214E-02 at 180iterations finished qdiffx linear iterations at : 13:20:42 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 8.4568153E-04 1.6485214E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 13:20:42 13.348u 0.243s 0:13.89 97.7% 0+0k 0+0io 0pf+0w