Mon Oct 10 09:46:19 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 09:46:19 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2924 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5687265 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): 114.3660 176.9620 ymin,ymax (A): -43.08100 10.42500 zmin,zma (A): 46.50000 102.8010 x,y,z range (A): 62.59599 53.50600 56.30099 scale (grids/A): 0.5687265 object centre (A): 145.6640 -16.32800 74.65050 number of atom coordinates read : 2924 total number of charged atoms : 2771 net assigned charge : 8.014020 assigned positive charge : 429.2528 centred at (gu) : 89.75233 89.07533 89.65112 assigned negative charge : -421.2393 centred at (gu) : 89.72508 89.14811 89.45850 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6441 nv = 96 ne = 84 npr = 55588 no. pairs analyzed = 55588 no. exposed pairs = 4527 no. arc points = 33318 no. surface atoms = 1486 nbur = 1438 mkacc time = 0.1200000 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 = 1.512000 m= 328 mr = 2749 m= 4 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3200000 number of dielectric boundary points 4015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3240 ## 383 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8145 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7810791E-09 3.5504897E-09 midg,1,midg; midg,igrid,midg 2.7479021E-09 1.1577352E-10 1,midg,midg; igrid,midg,midg 8.3366442E-10 1.4768382E-09 gauss-seidel spectral radius is 0.9840658 estimated iterations to convergence 65 setup time was (sec) 0.5400000 now iterating at: 09:46:19 rms-change max change #iterations 8.9274868E-02 14.19944 at 10iterations 6.6195251E-03 0.9740219 at 20iterations 4.8331506E-04 7.9303741E-02 at 30iterations 4.0786221E-05 5.4950714E-03 at 40iterations 6.1853980E-06 8.8834763E-04 at 50iterations finished qdiffx linear iterations at : 09:46:22 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 6.1853980E-06 8.8834763E-04 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 09:46:23 3.331u 0.172s 0:03.79 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 Mon Oct 10 2011 at 09:46:23 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2924 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 1.706180 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): 114.3660 176.9620 ymin,ymax (A): -43.08100 10.42500 zmin,zma (A): 46.50000 102.8010 x,y,z range (A): 62.59599 53.50600 56.30099 scale (grids/A): 1.706180 object centre (A): 145.6640 -16.32800 74.65050 number of atom coordinates read : 2924 total number of charged atoms : 2771 net assigned charge : 8.014020 assigned positive charge : 429.2528 centred at (gu) : 89.25682 87.22578 88.95269 assigned negative charge : -421.2393 centred at (gu) : 89.17496 87.44396 88.37503 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33318 grid for indexing accessible points = 1.400000 m= 21629 mr = 40664 m= 2797 mr = 13612 m= 96 mr = 1203 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 133 time to turn everything in is 0.5000000 number of dielectric boundary points 37334 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 305 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 21415 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) : 0.5687265 object centre at (A) : 145.6640 -16.32800 74.65050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6979691E-03 2.8395532E-02 midg,1,midg; midg,igrid,midg 9.4029913E-03 7.0542730E-03 1,midg,midg; igrid,midg,midg 7.0702904E-03 1.3048236E-02 gauss-seidel spectral radius is 0.9983707 estimated iterations to convergence 197 setup time was (sec) 0.7800000 now iterating at: 09:46:24 rms-change max change #iterations 3.569533 167.2860 at 10iterations 1.549200 58.46153 at 20iterations 0.6736519 26.94291 at 30iterations 0.2934555 11.71799 at 40iterations 0.1281969 4.283724 at 50iterations 5.5359405E-02 2.269994 at 60iterations 2.4023639E-02 0.9060217 at 70iterations 1.0515523E-02 0.3741474 at 80iterations 4.5780200E-03 0.1575775 at 90iterations 1.9974688E-03 6.9591522E-02 at 100iterations 8.7053364E-04 3.0090332E-02 at 110iterations 3.8061774E-04 1.3680696E-02 at 120iterations finished qdiffx linear iterations at : 09:46:30 total time elapsed so far: 7.220000 # loops : 120 mean,max change (kT/e) : 3.8061774E-04 1.3680696E-02 energy calculations done at 7.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 09:46:31 7.425u 0.205s 0:07.90 96.4% 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 09:46:31 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2924 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.559270 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): 114.3660 176.9620 ymin,ymax (A): -43.08100 10.42500 zmin,zma (A): 46.50000 102.8010 x,y,z range (A): 62.59599 53.50600 56.30099 scale (grids/A): 2.559270 object centre (A): 145.6640 -16.32800 74.65050 number of atom coordinates read : 2924 total number of charged atoms : 2771 net assigned charge : 8.014020 assigned positive charge : 429.2528 centred at (gu) : 88.88528 85.83842 88.42917 assigned negative charge : -421.2393 centred at (gu) : 88.76249 86.16592 87.56249 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 157357 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33318 grid for indexing accessible points = 1.400000 m= 70723 mr = 100548 m= 23175 mr = 52112 m= 4279 mr = 16349 m= 343 mr = 2476 m= 12 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 480 time to turn everything in is 1.190000 number of dielectric boundary points 84304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 22144 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) : 1.706180 object centre at (A) : 145.6640 -16.32800 74.65050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6704574E-02 0.3913413 midg,1,midg; midg,igrid,midg 0.1391083 0.1216932 1,midg,midg; igrid,midg,midg 0.1392664 6.4054787E-02 gauss-seidel spectral radius is 0.9992167 estimated iterations to convergence 282 setup time was (sec) 1.500000 now iterating at: 09:46:32 rms-change max change #iterations 9.302090 268.6318 at 10iterations 5.497930 137.2001 at 20iterations 3.203639 85.58552 at 30iterations 1.851137 44.59420 at 40iterations 1.068997 23.45310 at 50iterations 0.6114763 14.26283 at 60iterations 0.3491239 7.802059 at 70iterations 0.1992649 4.490007 at 80iterations 0.1132344 2.476822 at 90iterations 6.4365171E-02 1.445612 at 100iterations 3.6583479E-02 0.9948578 at 110iterations 2.0734377E-02 0.4692996 at 120iterations 1.1755088E-02 0.2566280 at 130iterations 6.6604209E-03 0.1480389 at 140iterations 3.7656121E-03 8.2309246E-02 at 150iterations 2.1336344E-03 4.6072006E-02 at 160iterations 1.2084622E-03 2.6363373E-02 at 170iterations 6.8267609E-04 1.4629841E-02 at 180iterations finished qdiffx linear iterations at : 09:46:44 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 6.8267609E-04 1.4629841E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.40000 DelPhi exited at 09:46:44 13.402u 0.212s 0:13.90 97.9% 0+0k 0+0io 0pf+0w