Mon Oct 10 19:38:42 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 19:38:42 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 = 2475 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: 0.6196045 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): -18.08500 32.05100 ymin,ymax (A): -42.90700 10.85100 zmin,zma (A): 13.25100 70.70700 x,y,z range (A): 50.13600 53.75800 57.45600 scale (grids/A): 0.6196045 object centre (A): 6.982999 -16.02800 41.97900 number of atom coordinates read : 2475 total number of charged atoms : 2337 net assigned charge : 5.000031 assigned positive charge : 361.6861 centred at (gu) : 88.66154 92.18662 91.66940 assigned negative charge : -356.6870 centred at (gu) : 88.64232 92.19263 91.64671 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6491 nv = 96 ne = 84 npr = 49111 no. pairs analyzed = 49111 no. exposed pairs = 3367 no. arc points = 23982 no. surface atoms = 1127 nbur = 1348 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3311 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2335 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8307664E-09 7.6078557E-09 midg,1,midg; midg,igrid,midg 2.7066465E-09 5.7142300E-09 1,midg,midg; igrid,midg,midg 3.6854513E-09 3.8169259E-09 gauss-seidel spectral radius is 0.9865103 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 19:38:43 rms-change max change #iterations 0.1213140 19.22669 at 10iterations 1.1052491E-02 2.106987 at 20iterations 1.0185872E-03 0.1527452 at 30iterations 9.4831950E-05 1.3679504E-02 at 40iterations 9.1640795E-06 1.4114380E-03 at 50iterations finished qdiffx linear iterations at : 19:38:45 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 9.1640795E-06 1.4114380E-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 19:38:46 3.460u 0.150s 0:04.02 89.8% 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 19:38:46 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 = 2475 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: 1.858814 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): -18.08500 32.05100 ymin,ymax (A): -42.90700 10.85100 zmin,zma (A): 13.25100 70.70700 x,y,z range (A): 50.13600 53.75800 57.45600 scale (grids/A): 1.858814 object centre (A): 6.982999 -16.02800 41.97900 number of atom coordinates read : 2475 total number of charged atoms : 2337 net assigned charge : 5.000031 assigned positive charge : 361.6861 centred at (gu) : 85.98389 96.55936 95.00770 assigned negative charge : -356.6870 centred at (gu) : 85.92695 96.57787 94.94015 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23982 grid for indexing accessible points = 1.400000 m= 24025 mr = 46246 m= 3865 mr = 17192 m= 193 mr = 2265 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 32203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18372 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) : 0.6196045 object centre at (A) : 6.982999 -16.02800 41.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3104704E-03 1.9418009E-02 midg,1,midg; midg,igrid,midg 1.2290969E-02 -3.4111496E-03 1,midg,midg; igrid,midg,midg -5.1105120E-03 1.1163224E-02 gauss-seidel spectral radius is 0.9985613 estimated iterations to convergence 209 setup time was (sec) 0.5800000 now iterating at: 19:38:47 rms-change max change #iterations 3.842648 195.9349 at 10iterations 1.755097 61.55674 at 20iterations 0.8065724 25.73194 at 30iterations 0.3683672 12.71285 at 40iterations 0.1695920 5.930585 at 50iterations 7.7422768E-02 2.449325 at 60iterations 3.5440326E-02 1.368240 at 70iterations 1.6308125E-02 0.5319023 at 80iterations 7.4685398E-03 0.2422390 at 90iterations 3.4147995E-03 0.1419220 at 100iterations 1.5683838E-03 5.9250832E-02 at 110iterations 7.2404015E-04 2.6191711E-02 at 120iterations finished qdiffx linear iterations at : 19:38:54 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 7.2404015E-04 2.6191711E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 19:38:55 7.876u 0.193s 0:08.67 92.9% 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 Mon Oct 10 2011 at 19:38:55 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 = 2475 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.788220 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): -18.08500 32.05100 ymin,ymax (A): -42.90700 10.85100 zmin,zma (A): 13.25100 70.70700 x,y,z range (A): 50.13600 53.75800 57.45600 scale (grids/A): 2.788220 object centre (A): 6.982999 -16.02800 41.97900 number of atom coordinates read : 2475 total number of charged atoms : 2337 net assigned charge : 5.000031 assigned positive charge : 361.6861 centred at (gu) : 83.97583 99.83879 97.51154 assigned negative charge : -356.6870 centred at (gu) : 83.89047 99.86687 97.41028 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 161799 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23982 grid for indexing accessible points = 1.400000 m= 77502 mr = 113086 m= 28194 mr = 61818 m= 6771 mr = 22182 m= 860 mr = 4824 m= 38 mr = 494 m= 0 mr = 2 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 72758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 18694 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) : 1.858814 object centre at (A) : 6.982999 -16.02800 41.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8818308E-02 0.2324663 midg,1,midg; midg,igrid,midg 0.1638949 -6.1222877E-02 1,midg,midg; igrid,midg,midg -0.1323088 0.1516430 gauss-seidel spectral radius is 0.9992381 estimated iterations to convergence 286 setup time was (sec) 1.140000 now iterating at: 19:38:56 rms-change max change #iterations 9.184739 319.3948 at 10iterations 5.313571 122.8643 at 20iterations 3.057195 61.60945 at 30iterations 1.754913 36.32006 at 40iterations 1.005144 21.33011 at 50iterations 0.5771145 10.60505 at 60iterations 0.3295977 6.620980 at 70iterations 0.1886591 4.053807 at 80iterations 0.1073100 1.969992 at 90iterations 6.1082479E-02 1.238377 at 100iterations 3.4889329E-02 0.6699162 at 110iterations 1.9897915E-02 0.4246144 at 120iterations 1.1306710E-02 0.2132297 at 130iterations 6.4438540E-03 0.1190338 at 140iterations 3.6653911E-03 6.5776825E-02 at 150iterations 2.0881700E-03 3.8368702E-02 at 160iterations 1.1880470E-03 2.1446228E-02 at 170iterations 6.7731028E-04 1.3414383E-02 at 180iterations finished qdiffx linear iterations at : 19:39:08 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 6.7731028E-04 1.3414383E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 19:39:08 12.652u 0.205s 0:13.30 96.6% 0+0k 0+0io 0pf+0w