Sat Oct 8 19:09:23 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 Sat Oct 8 2011 at 19:09:23 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6243752 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): -31.93400 17.66800 ymin,ymax (A): -25.82300 21.34800 zmin,zma (A): -12.63600 44.38100 x,y,z range (A): 49.60200 47.17100 57.01700 scale (grids/A): 0.6243752 object centre (A): -7.133000 -2.237500 15.87250 number of atom coordinates read : 2599 total number of charged atoms : 2462 net assigned charge : 4.814007 assigned positive charge : 395.4120 centred at (gu) : 88.51186 89.23808 90.00754 assigned negative charge : -390.5986 centred at (gu) : 88.41254 89.28545 89.89424 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6829 nv = 96 ne = 84 npr = 52806 no. pairs analyzed = 52806 no. exposed pairs = 3125 no. arc points = 22016 no. surface atoms = 1049 nbur = 1550 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3829 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3000000 number of dielectric boundary points 3312 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2158 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8156 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1564872E-09 1.3004446E-08 midg,1,midg; midg,igrid,midg 9.5415880E-09 8.0581225E-10 1,midg,midg; igrid,midg,midg -4.4194737E-09 8.6554115E-09 gauss-seidel spectral radius is 0.9867154 estimated iterations to convergence 71 setup time was (sec) 0.5500000 now iterating at: 19:09:24 rms-change max change #iterations 0.1340427 22.83285 at 10iterations 1.2642594E-02 1.961945 at 20iterations 1.2012547E-03 0.1714554 at 30iterations 1.1903332E-04 1.7185211E-02 at 40iterations 1.2086505E-05 1.7566681E-03 at 50iterations finished qdiffx linear iterations at : 19:09:27 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.2086505E-05 1.7566681E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 19:09:27 3.328u 0.205s 0:03.81 92.3% 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 Sat Oct 8 2011 at 19:09:27 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.873125 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): -31.93400 17.66800 ymin,ymax (A): -25.82300 21.34800 zmin,zma (A): -12.63600 44.38100 x,y,z range (A): 49.60200 47.17100 57.01700 scale (grids/A): 1.873125 object centre (A): -7.133000 -2.237500 15.87250 number of atom coordinates read : 2599 total number of charged atoms : 2462 net assigned charge : 4.814007 assigned positive charge : 395.4120 centred at (gu) : 85.53506 87.71397 90.02204 assigned negative charge : -390.5986 centred at (gu) : 85.23736 87.85609 89.68246 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22016 grid for indexing accessible points = 1.400000 m= 27197 mr = 51580 m= 4290 mr = 20392 m= 217 mr = 2723 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2860 time to turn everything in is 0.5400000 number of dielectric boundary points 30510 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19347 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) : 0.6243752 object centre at (A) : -7.133000 -2.237500 15.87250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9576000E-02 2.8474787E-02 midg,1,midg; midg,igrid,midg 1.6691934E-02 3.2352044E-03 1,midg,midg; igrid,midg,midg 4.8227612E-05 3.5811465E-02 gauss-seidel spectral radius is 0.9985930 estimated iterations to convergence 211 setup time was (sec) 0.8200000 now iterating at: 19:09:28 rms-change max change #iterations 4.113103 169.9440 at 10iterations 1.901968 71.42555 at 20iterations 0.8834032 35.00779 at 30iterations 0.4065198 13.39650 at 40iterations 0.1893428 5.961908 at 50iterations 8.7565243E-02 2.586074 at 60iterations 4.0718880E-02 1.290586 at 70iterations 1.8833783E-02 0.6059675 at 80iterations 8.6966082E-03 0.2711000 at 90iterations 4.0334077E-03 0.1233215 at 100iterations 1.8683305E-03 5.6224823E-02 at 110iterations 8.6843374E-04 2.7128935E-02 at 120iterations finished qdiffx linear iterations at : 19:09:35 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 8.6843374E-04 2.7128935E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 19:09:35 7.392u 0.224s 0:07.93 95.9% 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 Sat Oct 8 2011 at 19:09:35 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.809688 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): -31.93400 17.66800 ymin,ymax (A): -25.82300 21.34800 zmin,zma (A): -12.63600 44.38100 x,y,z range (A): 49.60200 47.17100 57.01700 scale (grids/A): 2.809688 object centre (A): -7.133000 -2.237500 15.87250 number of atom coordinates read : 2599 total number of charged atoms : 2462 net assigned charge : 4.814007 assigned positive charge : 395.4120 centred at (gu) : 83.30244 86.57089 90.03290 assigned negative charge : -390.5986 centred at (gu) : 82.85598 86.78410 89.52370 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 169917 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22016 grid for indexing accessible points = 1.400000 m= 87745 mr = 124339 m= 32350 mr = 72786 m= 7675 mr = 26289 m= 1044 mr = 5857 m= 52 mr = 624 m= 0 mr = 9 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 9507 time to turn everything in is 1.310000 number of dielectric boundary points 68879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 19693 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) : 1.873125 object centre at (A) : -7.133000 -2.237500 15.87250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1062161 0.3046316 midg,1,midg; midg,igrid,midg 0.2009595 2.4490371E-02 1,midg,midg; igrid,midg,midg -5.3008017E-03 0.4535165 gauss-seidel spectral radius is 0.9992428 estimated iterations to convergence 287 setup time was (sec) 1.630000 now iterating at: 19:09:37 rms-change max change #iterations 9.655501 379.0247 at 10iterations 5.568850 143.7822 at 20iterations 3.205573 66.30905 at 30iterations 1.837787 38.97535 at 40iterations 1.053253 20.17418 at 50iterations 0.6014106 11.81244 at 60iterations 0.3443312 6.195065 at 70iterations 0.1967695 3.531002 at 80iterations 0.1124652 2.035797 at 90iterations 6.4226113E-02 1.208321 at 100iterations 3.6707517E-02 0.6530237 at 110iterations 2.0908110E-02 0.4083481 at 120iterations 1.1961711E-02 0.2476578 at 130iterations 6.8189870E-03 0.1266327 at 140iterations 3.8879621E-03 7.1219444E-02 at 150iterations 2.2235368E-03 3.9714813E-02 at 160iterations 1.2717672E-03 2.3202896E-02 at 170iterations 7.2861800E-04 1.3638496E-02 at 180iterations finished qdiffx linear iterations at : 19:09:47 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 7.2861800E-04 1.3638496E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 19:09:48 12.065u 0.226s 0:12.57 97.6% 0+0k 0+0io 0pf+0w