Tue Oct 11 03:13:46 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+sph2.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 = amb2.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 03:13:46 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 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: 0.6263416 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): -26.55100 23.71800 ymin,ymax (A): -21.68100 22.70700 zmin,zma (A): -24.79500 32.04300 x,y,z range (A): 50.26900 44.38800 56.83800 scale (grids/A): 0.6263416 object centre (A): -1.416499 0.5129995 3.624000 number of atom coordinates read : 2016 total number of charged atoms : 1875 net assigned charge : 4.000014 assigned positive charge : 294.8079 centred at (gu) : 92.15560 90.13606 88.45209 assigned negative charge : -290.8083 centred at (gu) : 92.22666 90.07384 88.55799 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5544 nv = 96 ne = 84 npr = 39515 no. pairs analyzed = 39515 no. exposed pairs = 2810 no. arc points = 20749 no. surface atoms = 938 nbur = 1078 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 291 mr = 2762 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1954 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6442 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4154369E-08 -1.7186561E-09 midg,1,midg; midg,igrid,midg 1.5115049E-10 7.7531572E-09 1,midg,midg; igrid,midg,midg 5.0720907E-09 -7.8513546E-10 gauss-seidel spectral radius is 0.9867576 estimated iterations to convergence 71 setup time was (sec) 0.3500000 now iterating at: 03:13:46 rms-change max change #iterations 0.1148049 18.97292 at 10iterations 1.0451755E-02 1.592475 at 20iterations 9.8006835E-04 0.1818242 at 30iterations 9.1304217E-05 1.6685963E-02 at 40iterations 8.6611080E-06 1.3885498E-03 at 50iterations finished qdiffx linear iterations at : 03:13:49 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 8.6611080E-06 1.3885498E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 03:13:50 3.375u 0.180s 0:03.88 91.4% 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 Tue Oct 11 2011 at 03:13:50 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 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: 1.879025 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): -26.55100 23.71800 ymin,ymax (A): -21.68100 22.70700 zmin,zma (A): -24.79500 32.04300 x,y,z range (A): 50.26900 44.38800 56.83800 scale (grids/A): 1.879025 object centre (A): -1.416499 0.5129995 3.624000 number of atom coordinates read : 2016 total number of charged atoms : 1875 net assigned charge : 4.000014 assigned positive charge : 294.8079 centred at (gu) : 96.46671 90.40837 85.35618 assigned negative charge : -290.8083 centred at (gu) : 96.68017 90.22166 85.67406 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 58672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20749 grid for indexing accessible points = 1.400000 m= 20159 mr = 37939 m= 2988 mr = 13997 m= 134 mr = 1620 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 28371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 14740 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) : 0.6263416 object centre at (A) : -1.416499 0.5129995 3.624000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5099397E-02 -2.9175473E-02 midg,1,midg; midg,igrid,midg -6.4692167E-03 7.0022340E-03 1,midg,midg; igrid,midg,midg 1.4862701E-02 4.8347386E-03 gauss-seidel spectral radius is 0.9985471 estimated iterations to convergence 208 setup time was (sec) 0.5100000 now iterating at: 03:13:50 rms-change max change #iterations 3.531778 181.6469 at 10iterations 1.609937 63.39810 at 20iterations 0.7325624 30.14935 at 30iterations 0.3344672 12.03128 at 40iterations 0.1518624 5.702183 at 50iterations 6.9352269E-02 2.450768 at 60iterations 3.1615157E-02 1.306718 at 70iterations 1.4400556E-02 0.6464022 at 80iterations 6.5968526E-03 0.2371364 at 90iterations 3.0010005E-03 0.1068611 at 100iterations 1.3677999E-03 4.9201965E-02 at 110iterations 6.2481419E-04 2.0709991E-02 at 120iterations finished qdiffx linear iterations at : 03:13:58 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 6.2481419E-04 2.0709991E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 03:13:58 7.731u 0.214s 0:08.26 96.1% 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 03:13:58 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 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: 2.818537 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): -26.55100 23.71800 ymin,ymax (A): -21.68100 22.70700 zmin,zma (A): -24.79500 32.04300 x,y,z range (A): 50.26900 44.38800 56.83800 scale (grids/A): 2.818537 object centre (A): -1.416499 0.5129995 3.624000 number of atom coordinates read : 2016 total number of charged atoms : 1875 net assigned charge : 4.000014 assigned positive charge : 294.8079 centred at (gu) : 99.69979 90.61261 83.03410 assigned negative charge : -290.8083 centred at (gu) : 100.0204 90.33249 83.51100 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 135381 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20749 grid for indexing accessible points = 1.400000 m= 64734 mr = 92260 m= 23008 mr = 51249 m= 5096 mr = 17605 m= 615 mr = 3485 m= 44 mr = 306 m= 0 mr = 10 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 63963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 14999 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) : 1.879025 object centre at (A) : -1.416499 0.5129995 3.624000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3188006 -0.4492925 midg,1,midg; midg,igrid,midg -6.6164061E-02 6.0013093E-02 1,midg,midg; igrid,midg,midg 0.1436527 7.1428739E-02 gauss-seidel spectral radius is 0.9992389 estimated iterations to convergence 286 setup time was (sec) 1.000000 now iterating at: 03:13:59 rms-change max change #iterations 8.609897 413.9884 at 10iterations 5.030964 135.6078 at 20iterations 2.910914 77.32391 at 30iterations 1.679639 41.18793 at 40iterations 0.9685667 20.83741 at 50iterations 0.5550383 13.00262 at 60iterations 0.3190557 7.347237 at 70iterations 0.1820136 4.002774 at 80iterations 0.1039813 2.374238 at 90iterations 5.9364818E-02 1.405207 at 100iterations 3.3899695E-02 0.7340736 at 110iterations 1.9300176E-02 0.3933225 at 120iterations 1.1002092E-02 0.2312803 at 130iterations 6.2642684E-03 0.1340637 at 140iterations 3.5639140E-03 6.7146420E-02 at 150iterations 2.0312218E-03 4.0694118E-02 at 160iterations 1.1582851E-03 2.3557663E-02 at 170iterations 6.6030928E-04 1.3860703E-02 at 180iterations finished qdiffx linear iterations at : 03:14:10 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 6.6030928E-04 1.3860703E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 03:14:11 12.313u 0.209s 0:12.86 97.2% 0+0k 0+0io 0pf+0w