Mon Oct 10 17:14:47 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 Mon Oct 10 2011 at 17:14:47 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 = 2872 !!! WARNING: ASN 315 has a net charge of -0.0550 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: 0.6066803 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): -33.10800 22.41900 ymin,ymax (A): 40.26600 90.08900 zmin,zma (A): 0.3040000 58.98400 x,y,z range (A): 55.52700 49.82299 58.68000 scale (grids/A): 0.6066803 object centre (A): -5.344501 65.17750 29.64400 number of atom coordinates read : 2872 total number of charged atoms : 2728 net assigned charge : -0.5549893 assigned positive charge : 428.2882 centred at (gu) : 91.59787 89.34234 88.93842 assigned negative charge : -428.8439 centred at (gu) : 91.55354 89.39975 88.89771 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7135 nv = 96 ne = 84 npr = 56899 no. pairs analyzed = 56899 no. exposed pairs = 3943 no. arc points = 26779 no. surface atoms = 1308 nbur = 1564 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3743 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2632 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8787 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9886125E-09 1.3075311E-09 midg,1,midg; midg,igrid,midg 2.8895664E-09 -2.7349814E-09 1,midg,midg; igrid,midg,midg -1.7603000E-09 2.6778453E-09 gauss-seidel spectral radius is 0.9859653 estimated iterations to convergence 69 setup time was (sec) 0.5500000 now iterating at: 17:14:48 rms-change max change #iterations 0.1166820 18.19730 at 10iterations 1.0242713E-02 1.675622 at 20iterations 9.5639989E-04 0.1357636 at 30iterations 1.0299429E-04 1.6205788E-02 at 40iterations 1.7926637E-05 2.6540756E-03 at 50iterations finished qdiffx linear iterations at : 17:14:50 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.7926637E-05 2.6540756E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 17:14:51 3.163u 0.170s 0:04.20 79.2% 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 Mon Oct 10 2011 at 17:14:51 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 = 2872 !!! WARNING: ASN 315 has a net charge of -0.0550 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: 1.820041 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): -33.10800 22.41900 ymin,ymax (A): 40.26600 90.08900 zmin,zma (A): 0.3040000 58.98400 x,y,z range (A): 55.52700 49.82299 58.68000 scale (grids/A): 1.820041 object centre (A): -5.344501 65.17750 29.64400 number of atom coordinates read : 2872 total number of charged atoms : 2728 net assigned charge : -0.5549893 assigned positive charge : 428.2882 centred at (gu) : 94.79319 88.02638 86.81425 assigned negative charge : -428.8439 centred at (gu) : 94.66012 88.19870 86.69268 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77200 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26779 grid for indexing accessible points = 1.400000 m= 26111 mr = 52104 m= 3691 mr = 18437 m= 168 mr = 2094 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 180 time to turn everything in is 0.5400000 number of dielectric boundary points 34505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21331 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) : 0.6066803 object centre at (A) : -5.344501 65.17750 29.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3074519E-02 -4.6130132E-02 midg,1,midg; midg,igrid,midg 6.6031213E-03 -4.6847446E-04 1,midg,midg; igrid,midg,midg -1.4504034E-02 1.0399188E-02 gauss-seidel spectral radius is 0.9985443 estimated iterations to convergence 208 setup time was (sec) 0.8100000 now iterating at: 17:14:52 rms-change max change #iterations 4.079993 169.2059 at 10iterations 1.853130 70.32993 at 20iterations 0.8470305 26.91476 at 30iterations 0.3873447 12.53450 at 40iterations 0.1761989 5.626278 at 50iterations 8.0517605E-02 2.685257 at 60iterations 3.6706034E-02 1.137701 at 70iterations 1.6774919E-02 0.4873915 at 80iterations 7.6742950E-03 0.2822666 at 90iterations 3.5129318E-03 0.1209402 at 100iterations 1.6061758E-03 4.9530029E-02 at 110iterations 7.3342834E-04 2.2403717E-02 at 120iterations finished qdiffx linear iterations at : 17:14:58 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 7.3342834E-04 2.2403717E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.910000 DelPhi exited at 17:14:59 6.917u 0.163s 0:07.40 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 Mon Oct 10 2011 at 17:14:59 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 = 2872 !!! WARNING: ASN 315 has a net charge of -0.0550 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: 2.730062 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): -33.10800 22.41900 ymin,ymax (A): 40.26600 90.08900 zmin,zma (A): 0.3040000 58.98400 x,y,z range (A): 55.52700 49.82299 58.68000 scale (grids/A): 2.730062 object centre (A): -5.344501 65.17750 29.64400 number of atom coordinates read : 2872 total number of charged atoms : 2728 net assigned charge : -0.5549893 assigned positive charge : 428.2882 centred at (gu) : 97.18953 87.03933 85.22131 assigned negative charge : -428.8439 centred at (gu) : 96.98984 87.29796 85.03875 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 178739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26779 grid for indexing accessible points = 1.400000 m= 86199 mr = 127294 m= 28898 mr = 68417 m= 6283 mr = 22434 m= 709 mr = 4423 m= 27 mr = 417 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 613 time to turn everything in is 1.310000 number of dielectric boundary points 77870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 21823 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) : 1.820041 object centre at (A) : -5.344501 65.17750 29.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3780501 -0.8814477 midg,1,midg; midg,igrid,midg 6.2283147E-02 -1.0032089E-02 1,midg,midg; igrid,midg,midg -9.2762701E-02 0.2182763 gauss-seidel spectral radius is 0.9992481 estimated iterations to convergence 288 setup time was (sec) 1.590000 now iterating at: 17:15:01 rms-change max change #iterations 10.00409 300.9009 at 10iterations 5.914678 148.8274 at 20iterations 3.462629 87.35474 at 30iterations 2.015980 53.53495 at 40iterations 1.169167 24.16189 at 50iterations 0.6762416 13.82164 at 60iterations 0.3909237 7.772388 at 70iterations 0.2247883 4.355978 at 80iterations 0.1297754 2.679805 at 90iterations 7.4297935E-02 1.450607 at 100iterations 4.2689618E-02 0.8406067 at 110iterations 2.4536451E-02 0.4553471 at 120iterations 1.4063396E-02 0.2900906 at 130iterations 8.0620991E-03 0.1508871 at 140iterations 4.6154256E-03 8.1727028E-02 at 150iterations 2.6448264E-03 4.7248840E-02 at 160iterations 1.5128963E-03 2.6458740E-02 at 170iterations 8.6883205E-04 1.5743256E-02 at 180iterations finished qdiffx linear iterations at : 17:15:10 total time elapsed so far: 11.17000 # loops : 180 mean,max change (kT/e) : 8.6883205E-04 1.5743256E-02 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 17:15:11 11.349u 0.172s 0:11.87 96.9% 0+0k 0+0io 0pf+0w