Mon Oct 10 14:08:58 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 Mon Oct 10 2011 at 14:08:58 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2853 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: 0.6107917 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): 6.917000 60.99400 ymin,ymax (A): -19.44700 38.83800 zmin,zma (A): 38.53300 87.68600 x,y,z range (A): 54.07700 58.28500 49.15301 scale (grids/A): 0.6107917 object centre (A): 33.95550 9.695500 63.10950 number of atom coordinates read : 2853 total number of charged atoms : 2702 net assigned charge : -2.999974 assigned positive charge : 437.8613 centred at (gu) : 89.24754 89.45887 90.79942 assigned negative charge : -440.8621 centred at (gu) : 89.40935 89.60172 90.56639 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7056 nv = 96 ne = 84 npr = 57186 no. pairs analyzed = 57186 no. exposed pairs = 3469 no. arc points = 24227 no. surface atoms = 1172 nbur = 1681 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3945 m= 2 mr = 44 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 0.3200000 number of dielectric boundary points 3411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2398 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8694 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3198689E-08 1.3264160E-08 midg,1,midg; midg,igrid,midg 6.8692176E-09 -9.1969401E-09 1,midg,midg; igrid,midg,midg 8.4673770E-09 -9.7241504E-09 gauss-seidel spectral radius is 0.9861410 estimated iterations to convergence 70 setup time was (sec) 0.5500000 now iterating at: 14:08:58 rms-change max change #iterations 0.1287876 21.28134 at 10iterations 1.1371436E-02 1.619068 at 20iterations 1.0196170E-03 0.1749582 at 30iterations 8.9529596E-05 1.2353897E-02 at 40iterations 8.9603664E-06 1.3103485E-03 at 50iterations finished qdiffx linear iterations at : 14:09:01 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 8.9603664E-06 1.3103485E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 14:09:02 3.199u 0.159s 0:04.15 80.4% 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 Mon Oct 10 2011 at 14:09:02 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2853 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: 1.832375 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): 6.917000 60.99400 ymin,ymax (A): -19.44700 38.83800 zmin,zma (A): 38.53300 87.68600 x,y,z range (A): 54.07700 58.28500 49.15301 scale (grids/A): 1.832375 object centre (A): 33.95550 9.695500 63.10950 number of atom coordinates read : 2853 total number of charged atoms : 2702 net assigned charge : -2.999974 assigned positive charge : 437.8613 centred at (gu) : 87.74209 88.37584 92.39751 assigned negative charge : -440.8621 centred at (gu) : 88.22762 88.80473 91.69885 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24227 grid for indexing accessible points = 1.400000 m= 27167 mr = 53984 m= 3962 mr = 20089 m= 177 mr = 2389 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 257 time to turn everything in is 0.5500000 number of dielectric boundary points 31595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21142 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) : 0.6107917 object centre at (A) : 33.95550 9.695500 63.10950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1695067E-02 1.8946853E-02 midg,1,midg; midg,igrid,midg 0.1043931 -3.7297215E-03 1,midg,midg; igrid,midg,midg -5.2696728E-04 -2.8463610E-02 gauss-seidel spectral radius is 0.9985515 estimated iterations to convergence 208 setup time was (sec) 0.8200000 now iterating at: 14:09:03 rms-change max change #iterations 4.211426 174.5917 at 10iterations 1.926805 71.20596 at 20iterations 0.8820096 37.32956 at 30iterations 0.4066250 12.89652 at 40iterations 0.1862480 6.147972 at 50iterations 8.5501738E-02 2.727662 at 60iterations 3.9165635E-02 1.162869 at 70iterations 1.8023171E-02 0.5231876 at 80iterations 8.2973503E-03 0.2526703 at 90iterations 3.8200631E-03 0.1162460 at 100iterations 1.7802693E-03 5.8349609E-02 at 110iterations 8.4163138E-04 3.2183647E-02 at 120iterations finished qdiffx linear iterations at : 14:09:09 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 8.4163138E-04 3.2183647E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 14:09:10 7.516u 0.238s 0:08.19 94.5% 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 14:09:10 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2853 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: 2.748563 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): 6.917000 60.99400 ymin,ymax (A): -19.44700 38.83800 zmin,zma (A): 38.53300 87.68600 x,y,z range (A): 54.07700 58.28500 49.15301 scale (grids/A): 2.748563 object centre (A): 33.95550 9.695500 63.10950 number of atom coordinates read : 2853 total number of charged atoms : 2702 net assigned charge : -2.999974 assigned positive charge : 437.8613 centred at (gu) : 86.61297 87.56365 93.59617 assigned negative charge : -440.8621 centred at (gu) : 87.34131 88.20708 92.54811 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 177855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24227 grid for indexing accessible points = 1.400000 m= 89221 mr = 131024 m= 30903 mr = 73159 m= 6968 mr = 24809 m= 836 mr = 5147 m= 26 mr = 506 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 839 time to turn everything in is 1.350000 number of dielectric boundary points 71156 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 21614 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) : 1.832375 object centre at (A) : 33.95550 9.695500 63.10950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7003129 0.1497604 midg,1,midg; midg,igrid,midg 1.229630 -0.2287647 1,midg,midg; igrid,midg,midg -4.0795986E-02 -0.2296867 gauss-seidel spectral radius is 0.9992425 estimated iterations to convergence 287 setup time was (sec) 1.650000 now iterating at: 14:09:12 rms-change max change #iterations 10.06991 302.8665 at 10iterations 5.866413 132.2483 at 20iterations 3.393425 68.82172 at 30iterations 1.964387 43.32067 at 40iterations 1.128471 25.83768 at 50iterations 0.6486694 12.97887 at 60iterations 0.3714869 9.139579 at 70iterations 0.2127202 3.753241 at 80iterations 0.1221629 2.135066 at 90iterations 6.9819130E-02 1.270870 at 100iterations 3.9910961E-02 0.7549534 at 110iterations 2.2866799E-02 0.4213848 at 120iterations 1.3071894E-02 0.2360001 at 130iterations 7.4560288E-03 0.1412144 at 140iterations 4.2719790E-03 7.6448441E-02 at 150iterations 2.4405294E-03 4.2182922E-02 at 160iterations 1.3965679E-03 2.4581909E-02 at 170iterations 8.0023042E-04 1.5707016E-02 at 180iterations finished qdiffx linear iterations at : 14:09:23 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 8.0023042E-04 1.5707016E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 14:09:23 12.373u 0.224s 0:13.12 95.9% 0+0k 0+0io 0pf+0w