Sat Oct 8 21:02:09 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 Sat Oct 8 2011 at 21:02:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 444 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6179376 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): -31.35400 17.19400 ymin,ymax (A): -23.11400 23.83400 zmin,zma (A): -12.56900 45.04200 x,y,z range (A): 48.54800 46.94800 57.61100 scale (grids/A): 0.6179376 object centre (A): -7.080000 0.3599997 16.23650 number of atom coordinates read : 2600 total number of charged atoms : 2461 net assigned charge : 4.000009 assigned positive charge : 392.1620 centred at (gu) : 88.57169 88.82188 89.75578 assigned negative charge : -388.1625 centred at (gu) : 88.47916 88.86219 89.62441 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6441 nv = 96 ne = 84 npr = 54548 no. pairs analyzed = 54548 no. exposed pairs = 2990 no. arc points = 21281 no. surface atoms = 1013 nbur = 1587 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3618 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.1800000 number of dielectric boundary points 3111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2074 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8007 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5163398E-09 1.0586660E-08 midg,1,midg; midg,igrid,midg 7.2685920E-09 4.7601706E-10 1,midg,midg; igrid,midg,midg -3.8468833E-09 6.4448997E-09 gauss-seidel spectral radius is 0.9864333 estimated iterations to convergence 70 setup time was (sec) 0.3700000 now iterating at: 21:02:10 rms-change max change #iterations 0.1260953 20.60795 at 10iterations 1.1554713E-02 1.987318 at 20iterations 1.0748632E-03 0.1731396 at 30iterations 1.0716727E-04 2.0669937E-02 at 40iterations 1.1190004E-05 1.8997192E-03 at 50iterations finished qdiffx linear iterations at : 21:02:13 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1190004E-05 1.8997192E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 21:02:13 3.349u 0.182s 0:03.85 91.4% 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 Sat Oct 8 2011 at 21:02:13 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 444 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.853813 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): -31.35400 17.19400 ymin,ymax (A): -23.11400 23.83400 zmin,zma (A): -12.56900 45.04200 x,y,z range (A): 48.54800 46.94800 57.61100 scale (grids/A): 1.853813 object centre (A): -7.080000 0.3599997 16.23650 number of atom coordinates read : 2600 total number of charged atoms : 2461 net assigned charge : 4.000009 assigned positive charge : 392.1620 centred at (gu) : 85.71468 86.46523 89.26685 assigned negative charge : -388.1625 centred at (gu) : 85.43742 86.58628 88.87292 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70333 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21281 grid for indexing accessible points = 1.400000 m= 24227 mr = 49555 m= 3417 mr = 17816 m= 142 mr = 1998 m= 4 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3744 time to turn everything in is 0.3400000 number of dielectric boundary points 28720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19280 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) : 0.6179376 object centre at (A) : -7.080000 0.3599997 16.23650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2640688E-02 2.2001827E-02 midg,1,midg; midg,igrid,midg 1.4861331E-02 3.7899986E-03 1,midg,midg; igrid,midg,midg -1.2567956E-03 2.9908095E-02 gauss-seidel spectral radius is 0.9985546 estimated iterations to convergence 209 setup time was (sec) 0.5500000 now iterating at: 21:02:14 rms-change max change #iterations 4.007790 194.1974 at 10iterations 1.843466 64.57196 at 20iterations 0.8441973 27.58747 at 30iterations 0.3852026 13.16991 at 40iterations 0.1775087 5.634827 at 50iterations 8.1702694E-02 2.514099 at 60iterations 3.7375581E-02 1.288656 at 70iterations 1.7120207E-02 0.6193714 at 80iterations 7.8524407E-03 0.2757292 at 90iterations 3.6125346E-03 0.1387043 at 100iterations 1.6535990E-03 5.8053970E-02 at 110iterations 7.6045963E-04 2.3399353E-02 at 120iterations finished qdiffx linear iterations at : 21:02:22 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 7.6045963E-04 2.3399353E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 21:02:22 7.665u 0.987s 0:09.07 95.2% 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 21:02:22 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 444 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.780719 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): -31.35400 17.19400 ymin,ymax (A): -23.11400 23.83400 zmin,zma (A): -12.56900 45.04200 x,y,z range (A): 48.54800 46.94800 57.61100 scale (grids/A): 2.780719 object centre (A): -7.080000 0.3599997 16.23650 number of atom coordinates read : 2600 total number of charged atoms : 2461 net assigned charge : 4.000009 assigned positive charge : 392.1620 centred at (gu) : 83.57195 84.69769 88.90017 assigned negative charge : -388.1625 centred at (gu) : 83.15611 84.87932 88.30943 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 162952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21281 grid for indexing accessible points = 1.400000 m= 80603 mr = 119858 m= 26977 mr = 66464 m= 6099 mr = 21432 m= 620 mr = 4464 m= 20 mr = 324 m= 0 mr = 7 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 12700 time to turn everything in is 0.8800000 number of dielectric boundary points 64722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 19684 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) : 1.853813 object centre at (A) : -7.080000 0.3599997 16.23650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1338102 0.2342508 midg,1,midg; midg,igrid,midg 0.1614646 1.1383073E-02 1,midg,midg; igrid,midg,midg 2.0233329E-02 0.3817791 gauss-seidel spectral radius is 0.9992290 estimated iterations to convergence 284 setup time was (sec) 1.110000 now iterating at: 21:02:24 rms-change max change #iterations 9.450953 452.1495 at 10iterations 5.425728 110.4059 at 20iterations 3.106581 74.26038 at 30iterations 1.767051 34.62165 at 40iterations 1.007796 22.24796 at 50iterations 0.5746874 11.52515 at 60iterations 0.3266377 6.991864 at 70iterations 0.1860669 3.871963 at 80iterations 0.1057653 2.127850 at 90iterations 5.9987709E-02 1.214775 at 100iterations 3.4098908E-02 0.6876888 at 110iterations 1.9382188E-02 0.4034996 at 120iterations 1.1040197E-02 0.2176819 at 130iterations 6.2746112E-03 0.1189737 at 140iterations 3.5637706E-03 6.9321632E-02 at 150iterations 2.0365040E-03 4.0737152E-02 at 160iterations 1.1599204E-03 2.3654938E-02 at 170iterations 6.6389889E-04 1.3513565E-02 at 180iterations finished qdiffx linear iterations at : 21:02:35 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 6.6389889E-04 1.3513565E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 21:02:35 12.324u 0.244s 0:13.04 96.3% 0+0k 0+0io 0pf+0w