Sun Oct 9 10:40:59 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 Sun Oct 9 2011 at 10:40:59 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 !!! WARNING: HIR 216 has a net charge of 0.5140 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: 0.6167599 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): -69.95900 -18.53700 ymin,ymax (A): 7.919000 61.96100 zmin,zma (A): -30.06000 27.66100 x,y,z range (A): 51.42200 54.04200 57.72100 scale (grids/A): 0.6167599 object centre (A): -44.24800 34.94000 -1.199500 number of atom coordinates read : 2822 total number of charged atoms : 2679 net assigned charge : -0.4859836 assigned positive charge : 414.5341 centred at (gu) : 90.03886 92.03594 90.94762 assigned negative charge : -415.0217 centred at (gu) : 90.10748 92.02869 90.96483 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7518 nv = 96 ne = 84 npr = 55162 no. pairs analyzed = 55162 no. exposed pairs = 3970 no. arc points = 28333 no. surface atoms = 1313 nbur = 1509 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 410 mr = 3804 m= 2 mr = 49 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 0.2900000 number of dielectric boundary points 4077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2748 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8989 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0784588E-10 -1.8018140E-09 midg,1,midg; midg,igrid,midg -5.2309285E-10 2.0005034E-10 1,midg,midg; igrid,midg,midg 3.9951349E-09 -4.8380140E-09 gauss-seidel spectral radius is 0.9864260 estimated iterations to convergence 70 setup time was (sec) 0.5300000 now iterating at: 10:40:59 rms-change max change #iterations 0.1271305 19.29497 at 10iterations 1.1291740E-02 1.745441 at 20iterations 1.0425763E-03 0.1635323 at 30iterations 1.1987011E-04 1.8113613E-02 at 40iterations 2.5645179E-05 4.5978427E-03 at 50iterations finished qdiffx linear iterations at : 10:41:02 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 2.5645179E-05 4.5978427E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 10:41:03 3.356u 0.209s 0:03.94 90.1% 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 Sun Oct 9 2011 at 10:41:03 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 !!! WARNING: HIR 216 has a net charge of 0.5140 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: 1.850280 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): -69.95900 -18.53700 ymin,ymax (A): 7.919000 61.96100 zmin,zma (A): -30.06000 27.66100 x,y,z range (A): 51.42200 54.04200 57.72100 scale (grids/A): 1.850280 object centre (A): -44.24800 34.94000 -1.199500 number of atom coordinates read : 2822 total number of charged atoms : 2679 net assigned charge : -0.4859836 assigned positive charge : 414.5341 centred at (gu) : 90.11588 96.10689 92.84186 assigned negative charge : -415.0217 centred at (gu) : 90.32241 96.08590 92.89433 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81258 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28333 grid for indexing accessible points = 1.400000 m= 28614 mr = 53767 m= 4488 mr = 20085 m= 232 mr = 2591 m= 2 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 38071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 21003 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) : 0.6167599 object centre at (A) : -44.24800 34.94000 -1.199500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5380937E-02 -6.6332617E-03 midg,1,midg; midg,igrid,midg -1.2854866E-02 -1.2492868E-02 1,midg,midg; igrid,midg,midg 1.6464768E-02 -2.7981395E-02 gauss-seidel spectral radius is 0.9986090 estimated iterations to convergence 213 setup time was (sec) 0.8700000 now iterating at: 10:41:04 rms-change max change #iterations 4.202579 193.9922 at 10iterations 1.954622 68.25800 at 20iterations 0.9084786 29.22545 at 30iterations 0.4209596 12.92371 at 40iterations 0.1956715 6.618114 at 50iterations 9.1209106E-02 3.108080 at 60iterations 4.2393301E-02 1.384478 at 70iterations 1.9648796E-02 0.6723497 at 80iterations 9.1805886E-03 0.2933674 at 90iterations 4.2642644E-03 0.1278355 at 100iterations 1.9893541E-03 6.1943054E-02 at 110iterations 9.3049905E-04 2.9296875E-02 at 120iterations finished qdiffx linear iterations at : 10:41:10 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 9.3049905E-04 2.9296875E-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) 7.780000 DelPhi exited at 10:41:11 7.780u 0.233s 0:08.33 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 Sun Oct 9 2011 at 10:41:11 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 !!! WARNING: HIR 216 has a net charge of 0.5140 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: 2.775420 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): -69.95900 -18.53700 ymin,ymax (A): 7.919000 61.96100 zmin,zma (A): -30.06000 27.66100 x,y,z range (A): 51.42200 54.04200 57.72100 scale (grids/A): 2.775420 object centre (A): -44.24800 34.94000 -1.199500 number of atom coordinates read : 2822 total number of charged atoms : 2679 net assigned charge : -0.4859836 assigned positive charge : 414.5341 centred at (gu) : 90.17366 99.16013 94.26250 assigned negative charge : -415.0217 centred at (gu) : 90.48356 99.12885 94.34156 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 187931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28333 grid for indexing accessible points = 1.400000 m= 91675 mr = 131416 m= 33085 mr = 72354 m= 7965 mr = 25790 m= 1051 mr = 5680 m= 45 mr = 656 m= 0 mr = 22 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 85834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 21429 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) : 1.850280 object centre at (A) : -44.24800 34.94000 -1.199500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3375996 -5.1899809E-02 midg,1,midg; midg,igrid,midg -0.1508629 -0.1148356 1,midg,midg; igrid,midg,midg 0.2345624 -0.4021002 gauss-seidel spectral radius is 0.9992777 estimated iterations to convergence 294 setup time was (sec) 1.750000 now iterating at: 10:41:13 rms-change max change #iterations 10.19091 324.3730 at 10iterations 6.093976 147.3206 at 20iterations 3.606620 80.82866 at 30iterations 2.120965 43.69959 at 40iterations 1.243351 27.29575 at 50iterations 0.7265611 14.02254 at 60iterations 0.4250185 8.485591 at 70iterations 0.2470283 4.709106 at 80iterations 0.1436978 2.728806 at 90iterations 8.3345637E-02 1.528533 at 100iterations 4.8413362E-02 0.8754616 at 110iterations 2.8109353E-02 0.6139641 at 120iterations 1.6278835E-02 0.2905636 at 130iterations 9.4189253E-03 0.1671650 at 140iterations 5.4505984E-03 9.8074377E-02 at 150iterations 3.1601347E-03 6.1704636E-02 at 160iterations 1.8273272E-03 3.3252716E-02 at 170iterations 1.0568005E-03 1.7758846E-02 at 180iterations finished qdiffx linear iterations at : 10:41:24 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 1.0568005E-03 1.7758846E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 10:41:24 12.807u 0.255s 0:13.45 97.0% 0+0k 0+0io 0pf+0w