Tue Oct 11 04:24:31 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 04:24:31 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 = 2693 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: 0.6349093 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): -11.37000 36.82700 ymin,ymax (A): -26.79500 21.65500 zmin,zma (A): -10.36000 45.71100 x,y,z range (A): 48.19700 48.45000 56.07100 scale (grids/A): 0.6349093 object centre (A): 12.72850 -2.570001 17.67550 number of atom coordinates read : 2693 total number of charged atoms : 2545 net assigned charge : 1.500014 assigned positive charge : 406.5238 centred at (gu) : 90.13500 90.27440 91.98285 assigned negative charge : -405.0244 centred at (gu) : 89.86463 90.11268 91.94175 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7262 nv = 96 ne = 84 npr = 55190 no. pairs analyzed = 55190 no. exposed pairs = 3208 no. arc points = 22426 no. surface atoms = 1078 nbur = 1615 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 401 mr = 4188 m= 0 mr = 42 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2100000 number of dielectric boundary points 3433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2305 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8786 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6680173E-09 9.3493524E-09 midg,1,midg; midg,igrid,midg -1.4695893E-08 1.9640341E-08 1,midg,midg; igrid,midg,midg -2.6817787E-08 3.0303813E-08 gauss-seidel spectral radius is 0.9871534 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 04:24:31 rms-change max change #iterations 0.1444932 20.71000 at 10iterations 1.4242656E-02 2.112556 at 20iterations 1.4512389E-03 0.2009850 at 30iterations 1.8415452E-04 3.0944824E-02 at 40iterations 3.6083504E-05 5.2766800E-03 at 50iterations finished qdiffx linear iterations at : 04:24:34 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 3.6083504E-05 5.2766800E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 04:24:35 3.463u 0.158s 0:03.99 90.4% 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 04:24:35 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 = 2693 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: 1.904728 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): -11.37000 36.82700 ymin,ymax (A): -26.79500 21.65500 zmin,zma (A): -10.36000 45.71100 x,y,z range (A): 48.19700 48.45000 56.07100 scale (grids/A): 1.904728 object centre (A): 12.72850 -2.570001 17.67550 number of atom coordinates read : 2693 total number of charged atoms : 2545 net assigned charge : 1.500014 assigned positive charge : 406.5238 centred at (gu) : 90.40454 90.82274 95.94795 assigned negative charge : -405.0244 centred at (gu) : 89.59380 90.33778 95.82487 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22426 grid for indexing accessible points = 1.400000 m= 29624 mr = 55849 m= 4752 mr = 22510 m= 305 mr = 3131 m= 2 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 229 time to turn everything in is 0.4000000 number of dielectric boundary points 31615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20011 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) : 0.6349093 object centre at (A) : 12.72850 -2.570001 17.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2207303E-02 -8.0389017E-03 midg,1,midg; midg,igrid,midg -1.3120637E-02 2.1936433E-02 1,midg,midg; igrid,midg,midg -1.1211107E-02 5.6785785E-02 gauss-seidel spectral radius is 0.9986430 estimated iterations to convergence 215 setup time was (sec) 0.6100000 now iterating at: 04:24:36 rms-change max change #iterations 4.362711 178.5646 at 10iterations 2.057935 71.24312 at 20iterations 0.9684716 28.56035 at 30iterations 0.4562469 14.28244 at 40iterations 0.2136502 6.752779 at 50iterations 0.1009588 2.911560 at 60iterations 4.7392923E-02 1.654638 at 70iterations 2.2353398E-02 0.6543226 at 80iterations 1.0485317E-02 0.3320236 at 90iterations 4.9500740E-03 0.1808681 at 100iterations 2.3383121E-03 6.7335129E-02 at 110iterations 1.1041550E-03 3.5686493E-02 at 120iterations finished qdiffx linear iterations at : 04:24:43 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 1.1041550E-03 3.5686493E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 04:24:43 7.920u 0.204s 0:08.63 94.0% 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 04:24:44 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 = 2693 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: 2.857092 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): -11.37000 36.82700 ymin,ymax (A): -26.79500 21.65500 zmin,zma (A): -10.36000 45.71100 x,y,z range (A): 48.19700 48.45000 56.07100 scale (grids/A): 2.857092 object centre (A): 12.72850 -2.570001 17.67550 number of atom coordinates read : 2693 total number of charged atoms : 2545 net assigned charge : 1.500014 assigned positive charge : 406.5238 centred at (gu) : 90.60671 91.23408 98.92181 assigned negative charge : -405.0244 centred at (gu) : 89.39060 90.50676 98.73717 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 181366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22426 grid for indexing accessible points = 1.400000 m= 95303 mr = 134727 m= 35575 mr = 79479 m= 8611 mr = 29050 m= 1342 mr = 6729 m= 91 mr = 983 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 822 time to turn everything in is 1.020000 number of dielectric boundary points 71270 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 20358 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) : 1.904728 object centre at (A) : 12.72850 -2.570001 17.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5687541 0.1506538 midg,1,midg; midg,igrid,midg -0.1657842 0.2668183 1,midg,midg; igrid,midg,midg -8.3202392E-02 0.5189660 gauss-seidel spectral radius is 0.9992575 estimated iterations to convergence 290 setup time was (sec) 1.250000 now iterating at: 04:24:45 rms-change max change #iterations 10.19087 497.6559 at 10iterations 5.972240 139.5879 at 20iterations 3.478657 86.94479 at 30iterations 2.023376 44.37913 at 40iterations 1.173322 21.08626 at 50iterations 0.6782641 13.70081 at 60iterations 0.3910850 7.250474 at 70iterations 0.2256809 4.129242 at 80iterations 0.1301951 2.315981 at 90iterations 7.5292580E-02 1.384386 at 100iterations 4.3380383E-02 0.8179188 at 110iterations 2.4922453E-02 0.4322443 at 120iterations 1.4374965E-02 0.2651076 at 130iterations 8.3180005E-03 0.1434588 at 140iterations 4.8036114E-03 8.4430695E-02 at 150iterations 2.7933891E-03 5.1670074E-02 at 160iterations 1.6304187E-03 2.6584625E-02 at 170iterations 9.6768292E-04 1.8236160E-02 at 180iterations finished qdiffx linear iterations at : 04:24:56 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 9.6768292E-04 1.8236160E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 04:24:57 12.789u 0.213s 0:13.65 95.1% 0+0k 0+0io 0pf+0w