Wed Dec 28 11:04:15 PST 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 Wed Dec 28 2011 at 11:04:15 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 = 1964 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: 0.6396090 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): -5.443000 34.79500 ymin,ymax (A): -3.745000 48.32500 zmin,zma (A): -24.42500 31.23400 x,y,z range (A): 40.23800 52.07000 55.65900 scale (grids/A): 0.6396090 object centre (A): 14.67600 22.29000 3.404501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.74237 92.59457 90.15045 assigned negative charge : -285.8263 centred at (gu) : 90.86138 92.75652 90.08046 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5522 nv = 96 ne = 84 npr = 40372 no. pairs analyzed = 40372 no. exposed pairs = 2483 no. arc points = 17554 no. surface atoms = 836 nbur = 1128 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 3088 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1787 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6518 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5010118E-09 9.4991828E-09 midg,1,midg; midg,igrid,midg 9.6417194E-09 -1.8904753E-08 1,midg,midg; igrid,midg,midg 1.1289531E-08 -8.0369249E-09 gauss-seidel spectral radius is 0.9872804 estimated iterations to convergence 72 setup time was (sec) 0.4700000 now iterating at: 11:04:15 rms-change max change #iterations 0.1214098 19.40706 at 10iterations 1.2023082E-02 1.845343 at 20iterations 1.1857142E-03 0.2210312 at 30iterations 1.1718176E-04 2.0834446E-02 at 40iterations 1.1325730E-05 1.6593933E-03 at 50iterations finished qdiffx linear iterations at : 11:04:18 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 1.1325730E-05 1.6593933E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 11:04:19 3.159u 0.167s 0:03.78 87.5% 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 Wed Dec 28 2011 at 11:04:19 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.918827 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): -5.443000 34.79500 ymin,ymax (A): -3.745000 48.32500 zmin,zma (A): -24.42500 31.23400 x,y,z range (A): 40.23800 52.07000 55.65900 scale (grids/A): 1.918827 object centre (A): 14.67600 22.29000 3.404501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 92.22733 97.78384 90.45132 assigned negative charge : -285.8263 centred at (gu) : 92.58427 98.26968 90.24146 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59151 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17554 grid for indexing accessible points = 1.400000 m= 22490 mr = 40823 m= 3676 mr = 17289 m= 204 mr = 2441 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1308 time to turn everything in is 0.4800000 number of dielectric boundary points 24912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 14441 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) : 0.6396090 object centre at (A) : 14.67600 22.29000 3.404501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9748188E-02 1.0951918E-02 midg,1,midg; midg,igrid,midg 3.0445417E-02 -1.8459044E-02 1,midg,midg; igrid,midg,midg 7.8364974E-03 -5.2426145E-03 gauss-seidel spectral radius is 0.9985774 estimated iterations to convergence 210 setup time was (sec) 0.7400000 now iterating at: 11:04:20 rms-change max change #iterations 3.587156 164.2106 at 10iterations 1.652938 58.02636 at 20iterations 0.7634480 26.39887 at 30iterations 0.3531412 12.65139 at 40iterations 0.1621340 6.152348 at 50iterations 7.4668251E-02 2.622143 at 60iterations 3.4324799E-02 1.184552 at 70iterations 1.5825920E-02 0.5423737 at 80iterations 7.3067942E-03 0.2673130 at 90iterations 3.3588868E-03 0.1207114 at 100iterations 1.5473245E-03 5.6934357E-02 at 110iterations 7.1569375E-04 2.4387360E-02 at 120iterations finished qdiffx linear iterations at : 11:04:26 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 7.1569375E-04 2.4387360E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 11:04:26 6.952u 0.236s 0:07.74 92.7% 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 Wed Dec 28 2011 at 11:04:26 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.878241 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): -5.443000 34.79500 ymin,ymax (A): -3.745000 48.32500 zmin,zma (A): -24.42500 31.23400 x,y,z range (A): 40.23800 52.07000 55.65900 scale (grids/A): 2.878241 object centre (A): 14.67600 22.29000 3.404501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 93.34100 101.6758 90.67704 assigned negative charge : -285.8263 centred at (gu) : 93.87643 102.4047 90.36230 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 136432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17554 grid for indexing accessible points = 1.400000 m= 71114 mr = 98330 m= 27452 mr = 59413 m= 6767 mr = 22874 m= 879 mr = 5294 m= 47 mr = 608 m= 0 mr = 10 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 4607 time to turn everything in is 1.290000 number of dielectric boundary points 56162 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 14656 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) : 1.918827 object centre at (A) : 14.67600 22.29000 3.404501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9798901 -3.7940831E-03 midg,1,midg; midg,igrid,midg 0.3345641 -0.2019302 1,midg,midg; igrid,midg,midg 4.0917080E-02 -3.3873849E-02 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.730000 now iterating at: 11:04:29 rms-change max change #iterations 8.460341 488.5247 at 10iterations 4.856464 121.4332 at 20iterations 2.757343 59.65876 at 30iterations 1.565302 32.76963 at 40iterations 0.8886661 18.47659 at 50iterations 0.5054430 10.33043 at 60iterations 0.2859526 5.607690 at 70iterations 0.1623682 3.095051 at 80iterations 9.2175528E-02 1.901309 at 90iterations 5.2240405E-02 0.9787445 at 100iterations 2.9671872E-02 0.6170273 at 110iterations 1.6792858E-02 0.3534632 at 120iterations 9.5505761E-03 0.2040167 at 130iterations 5.4045613E-03 0.1062050 at 140iterations 3.0626941E-03 6.2162399E-02 at 150iterations 1.7373330E-03 3.5041809E-02 at 160iterations 9.8505954E-04 1.9317627E-02 at 170iterations 5.5866234E-04 1.0795593E-02 at 180iterations finished qdiffx linear iterations at : 11:04:41 total time elapsed so far: 13.78000 # loops : 180 mean,max change (kT/e) : 5.5866234E-04 1.0795593E-02 energy calculations done at 13.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.94000 DelPhi exited at 11:04:41 13.943u 0.433s 0:14.88 96.5% 0+0k 0+0io 0pf+0w