Mon Oct 10 13:59:48 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 Mon Oct 10 2011 at 13:59:49 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3364 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 0.5744345 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): -11.17000 50.80400 ymin,ymax (A): -12.56700 42.37700 zmin,zma (A): 19.55200 75.74200 x,y,z range (A): 61.97400 54.94400 56.19000 scale (grids/A): 0.5744345 object centre (A): 19.81700 14.90500 47.64700 number of atom coordinates read : 3364 total number of charged atoms : 3207 net assigned charge : 5.030018 assigned positive charge : 519.5958 centred at (gu) : 90.91321 89.95026 87.75420 assigned negative charge : -514.5671 centred at (gu) : 90.82799 90.01626 87.75244 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7432 nv = 96 ne = 84 npr = 65270 no. pairs analyzed = 65270 no. exposed pairs = 4485 no. arc points = 32061 no. surface atoms = 1508 nbur = 1856 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 378 mr = 3691 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3144 ## 347 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9314 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4178898E-09 5.5239641E-10 midg,1,midg; midg,igrid,midg 2.2830282E-09 -5.1017263E-10 1,midg,midg; igrid,midg,midg -7.3821227E-10 3.2964549E-09 gauss-seidel spectral radius is 0.9843987 estimated iterations to convergence 66 setup time was (sec) 0.6100000 now iterating at: 13:59:49 rms-change max change #iterations 9.7332045E-02 15.76617 at 10iterations 7.4950880E-03 1.321194 at 20iterations 5.7786959E-04 9.1201782E-02 at 30iterations 6.6073946E-05 1.0601044E-02 at 40iterations 2.6346632E-05 3.6516190E-03 at 50iterations finished qdiffx linear iterations at : 13:59:53 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 2.6346632E-05 3.6516190E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 13:59:54 4.275u 0.231s 0:05.21 86.3% 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 13:59:54 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3364 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.723303 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): -11.17000 50.80400 ymin,ymax (A): -12.56700 42.37700 zmin,zma (A): 19.55200 75.74200 x,y,z range (A): 61.97400 54.94400 56.19000 scale (grids/A): 1.723303 object centre (A): 19.81700 14.90500 47.64700 number of atom coordinates read : 3364 total number of charged atoms : 3207 net assigned charge : 5.030018 assigned positive charge : 519.5958 centred at (gu) : 92.73882 89.84983 83.26208 assigned negative charge : -514.5671 centred at (gu) : 92.48380 90.04851 83.25703 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 81037 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32061 grid for indexing accessible points = 1.400000 m= 27028 mr = 53986 m= 3496 mr = 18189 m= 159 mr = 1761 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 37750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 24846 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) : 0.5744345 object centre at (A) : 19.81700 14.90500 47.64700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7329829E-02 6.2813559E-03 midg,1,midg; midg,igrid,midg 2.3077920E-02 -6.3867164E-03 1,midg,midg; igrid,midg,midg -6.5084822E-03 -6.5698442E-03 gauss-seidel spectral radius is 0.9984213 estimated iterations to convergence 200 setup time was (sec) 1.050000 now iterating at: 13:59:55 rms-change max change #iterations 4.081751 180.3893 at 10iterations 1.805306 64.85090 at 20iterations 0.7989274 27.98828 at 30iterations 0.3535602 11.47090 at 40iterations 0.1569229 5.073422 at 50iterations 6.9970705E-02 2.517025 at 60iterations 3.0965511E-02 0.9643631 at 70iterations 1.3815967E-02 0.4426994 at 80iterations 6.1078887E-03 0.2205048 at 90iterations 2.7088418E-03 9.7541809E-02 at 100iterations 1.2127082E-03 3.7366867E-02 at 110iterations 5.4464815E-04 1.8142700E-02 at 120iterations finished qdiffx linear iterations at : 14:00:04 total time elapsed so far: 9.610000 # loops : 120 mean,max change (kT/e) : 5.4464815E-04 1.8142700E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.800000 DelPhi exited at 14:00:04 9.799u 0.277s 0:10.53 95.5% 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 14:00:04 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3364 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 2.584955 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): -11.17000 50.80400 ymin,ymax (A): -12.56700 42.37700 zmin,zma (A): 19.55200 75.74200 x,y,z range (A): 61.97400 54.94400 56.19000 scale (grids/A): 2.584955 object centre (A): 19.81700 14.90500 47.64700 number of atom coordinates read : 3364 total number of charged atoms : 3207 net assigned charge : 5.030018 assigned positive charge : 519.5958 centred at (gu) : 94.10814 89.77470 79.89278 assigned negative charge : -514.5671 centred at (gu) : 93.72552 90.07272 79.88544 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 188067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32061 grid for indexing accessible points = 1.400000 m= 89810 mr = 132712 m= 28849 mr = 69795 m= 5748 mr = 21346 m= 597 mr = 3763 m= 25 mr = 304 m= 0 mr = 8 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 85168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 25629 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) : 1.723303 object centre at (A) : 19.81700 14.90500 47.64700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2939129 7.7107176E-02 midg,1,midg; midg,igrid,midg 0.3604954 -8.4807128E-02 1,midg,midg; igrid,midg,midg 8.8614896E-02 -0.5461066 gauss-seidel spectral radius is 0.9992256 estimated iterations to convergence 284 setup time was (sec) 1.950000 now iterating at: 14:00:07 rms-change max change #iterations 10.52003 307.5263 at 10iterations 6.221997 172.0645 at 20iterations 3.640955 95.76749 at 30iterations 2.111545 58.78675 at 40iterations 1.218550 27.09157 at 50iterations 0.6997964 14.70263 at 60iterations 0.4024796 8.810766 at 70iterations 0.2300808 4.555357 at 80iterations 0.1318459 2.667163 at 90iterations 7.5240850E-02 1.577625 at 100iterations 4.2894654E-02 0.8563528 at 110iterations 2.4426114E-02 0.4851933 at 120iterations 1.3925732E-02 0.2930288 at 130iterations 7.9333531E-03 0.1681767 at 140iterations 4.5230570E-03 8.9473724E-02 at 150iterations 2.5836430E-03 4.7350168E-02 at 160iterations 1.4837738E-03 2.8686047E-02 at 170iterations 8.6835137E-04 1.6544342E-02 at 180iterations finished qdiffx linear iterations at : 14:00:22 total time elapsed so far: 17.53000 # loops : 180 mean,max change (kT/e) : 8.6835137E-04 1.6544342E-02 energy calculations done at 17.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.71000 DelPhi exited at 14:00:23 17.712u 0.454s 0:18.96 95.7% 0+0k 0+0io 0pf+0w