Tue Oct 11 08:20:03 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 Tue Oct 11 2011 at 08:20:03 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 = 2767 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: 0.6375473 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): -5.066000 50.77300 ymin,ymax (A): -16.16100 29.75800 zmin,zma (A): 57.62100 109.5750 x,y,z range (A): 55.83900 45.91900 51.95401 scale (grids/A): 0.6375473 object centre (A): 22.85350 6.798501 83.59800 number of atom coordinates read : 2767 total number of charged atoms : 2623 net assigned charge : 5.500018 assigned positive charge : 418.0574 centred at (gu) : 90.04826 90.20729 89.46542 assigned negative charge : -412.5582 centred at (gu) : 90.29253 90.13340 89.51414 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7516 nv = 96 ne = 84 npr = 56179 no. pairs analyzed = 56179 no. exposed pairs = 3262 no. arc points = 23112 no. surface atoms = 1110 nbur = 1657 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 4262 m= 4 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 101 time to turn everything in is 0.3300000 number of dielectric boundary points 3556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2230 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8998 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4665623E-08 1.6296219E-09 midg,1,midg; midg,igrid,midg -1.1051354E-09 1.6691434E-08 1,midg,midg; igrid,midg,midg 3.4692047E-08 -2.1875968E-08 gauss-seidel spectral radius is 0.9872668 estimated iterations to convergence 72 setup time was (sec) 0.5800000 now iterating at: 08:20:04 rms-change max change #iterations 0.1484925 27.61979 at 10iterations 1.5096495E-02 1.982460 at 20iterations 2.0507087E-03 0.3763275 at 30iterations 5.2608841E-04 0.1143570 at 40iterations 1.6147815E-04 3.6647797E-02 at 50iterations finished qdiffx linear iterations at : 08:20:06 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.6147815E-04 3.6647797E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 08:20:07 3.361u 0.134s 0:03.91 89.2% 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 Tue Oct 11 2011 at 08:20:07 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 = 2767 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.912642 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): -5.066000 50.77300 ymin,ymax (A): -16.16100 29.75800 zmin,zma (A): 57.62100 109.5750 x,y,z range (A): 55.83900 45.91900 51.95401 scale (grids/A): 1.912642 object centre (A): 22.85350 6.798501 83.59800 number of atom coordinates read : 2767 total number of charged atoms : 2623 net assigned charge : 5.500018 assigned positive charge : 418.0574 centred at (gu) : 90.14411 90.62095 88.39561 assigned negative charge : -412.5582 centred at (gu) : 90.87730 90.39973 88.54212 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23112 grid for indexing accessible points = 1.400000 m= 29209 mr = 57296 m= 4494 mr = 22098 m= 254 mr = 2934 m= 2 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 5246 time to turn everything in is 0.6000000 number of dielectric boundary points 32884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20663 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) : 0.6375473 object centre at (A) : 22.85350 6.798501 83.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0743986E-02 7.5470726E-03 midg,1,midg; midg,igrid,midg 1.4643079E-02 2.0898495E-02 1,midg,midg; igrid,midg,midg 5.1872123E-02 -3.9600395E-02 gauss-seidel spectral radius is 0.9986588 estimated iterations to convergence 216 setup time was (sec) 0.8700000 now iterating at: 08:20:08 rms-change max change #iterations 4.448731 179.2285 at 10iterations 2.087858 67.29539 at 20iterations 0.9819422 31.35593 at 30iterations 0.4637451 16.03970 at 40iterations 0.2189333 6.292842 at 50iterations 0.1032863 3.230829 at 60iterations 4.8800323E-02 1.488894 at 70iterations 2.3181589E-02 0.6932306 at 80iterations 1.1109432E-02 0.3309364 at 90iterations 5.3844294E-03 0.1656418 at 100iterations 2.6878698E-03 9.5726013E-02 at 110iterations 1.4045412E-03 5.3993225E-02 at 120iterations finished qdiffx linear iterations at : 08:20:14 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 1.4045412E-03 5.3993225E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 08:20:15 7.440u 0.171s 0:08.08 94.1% 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 Tue Oct 11 2011 at 08:20:15 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 = 2767 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.868963 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): -5.066000 50.77300 ymin,ymax (A): -16.16100 29.75800 zmin,zma (A): 57.62100 109.5750 x,y,z range (A): 55.83900 45.91900 51.95401 scale (grids/A): 2.868963 object centre (A): 22.85350 6.798501 83.59800 number of atom coordinates read : 2767 total number of charged atoms : 2623 net assigned charge : 5.500018 assigned positive charge : 418.0574 centred at (gu) : 90.21603 90.93111 87.59328 assigned negative charge : -412.5582 centred at (gu) : 91.31590 90.59960 87.81306 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 188279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23112 grid for indexing accessible points = 1.400000 m= 95385 mr = 138454 m= 33918 mr = 79284 m= 8016 mr = 27760 m= 1140 mr = 6303 m= 64 mr = 808 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 17783 time to turn everything in is 1.490000 number of dielectric boundary points 74166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 20982 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) : 1.912642 object centre at (A) : 22.85350 6.798501 83.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1791369E-02 5.2024918E-03 midg,1,midg; midg,igrid,midg 0.2218049 0.2269748 1,midg,midg; igrid,midg,midg 0.6159998 -0.3092580 gauss-seidel spectral radius is 0.9992605 estimated iterations to convergence 290 setup time was (sec) 1.780000 now iterating at: 08:20:17 rms-change max change #iterations 10.28481 352.0216 at 10iterations 5.957381 135.3990 at 20iterations 3.454243 60.48385 at 30iterations 1.992547 38.69448 at 40iterations 1.147544 20.25295 at 50iterations 0.6617789 11.32026 at 60iterations 0.3803300 6.435957 at 70iterations 0.2190048 3.799126 at 80iterations 0.1260669 2.288139 at 90iterations 7.2542571E-02 1.259151 at 100iterations 4.1751057E-02 0.7259197 at 110iterations 2.4075419E-02 0.4153061 at 120iterations 1.3899137E-02 0.2515221 at 130iterations 8.0901021E-03 0.1496868 at 140iterations 4.7485004E-03 9.0812683E-02 at 150iterations 2.8396752E-03 5.5107117E-02 at 160iterations 1.7578864E-03 3.9196014E-02 at 170iterations 1.1467995E-03 2.7606964E-02 at 180iterations finished qdiffx linear iterations at : 08:20:27 total time elapsed so far: 11.84000 # loops : 180 mean,max change (kT/e) : 1.1467995E-03 2.7606964E-02 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 08:20:28 12.025u 0.182s 0:12.55 97.2% 0+0k 0+0io 0pf+0w