Sat Oct 15 14:38:40 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 15 2011 at 14:38:40 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: HIT 107 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: 0.5865972 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): -26.44100 34.24800 ymin,ymax (A): 3.908000 51.68000 zmin,zma (A): -3.453000 55.61900 x,y,z range (A): 60.68900 47.77200 59.07200 scale (grids/A): 0.5865972 object centre (A): 3.903501 27.79400 26.08300 number of atom coordinates read : 3001 total number of charged atoms : 2859 net assigned charge : -2.485965 assigned positive charge : 457.6068 centred at (gu) : 90.22425 90.36900 89.54347 assigned negative charge : -460.0941 centred at (gu) : 90.32218 90.49621 89.46355 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6880 nv = 96 ne = 84 npr = 59518 no. pairs analyzed = 59518 no. exposed pairs = 4068 no. arc points = 28726 no. surface atoms = 1361 nbur = 1640 mkacc time = 0.1700000 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 = 1.456000 m= 314 mr = 3470 m= 0 mr = 15 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.4000000 number of dielectric boundary points 3709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2879 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8668 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2559693E-09 1.4303979E-09 midg,1,midg; midg,igrid,midg 2.6579150E-09 -4.6862074E-09 1,midg,midg; igrid,midg,midg 1.9857735E-09 -3.6322336E-09 gauss-seidel spectral radius is 0.9850072 estimated iterations to convergence 67 setup time was (sec) 0.6800000 now iterating at: 14:38:41 rms-change max change #iterations 0.1052739 15.70136 at 10iterations 8.3921924E-03 1.447350 at 20iterations 6.6432031E-04 9.5282078E-02 at 30iterations 5.5546087E-05 9.1590881E-03 at 40iterations 5.2731466E-06 7.9345703E-04 at 50iterations finished qdiffx linear iterations at : 14:38:44 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 5.2731466E-06 7.9345703E-04 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 14:38:45 4.252u 0.290s 0:04.83 93.9% 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 15 2011 at 14:38:45 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: HIT 107 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: 1.759792 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): -26.44100 34.24800 ymin,ymax (A): 3.908000 51.68000 zmin,zma (A): -3.453000 55.61900 x,y,z range (A): 60.68900 47.77200 59.07200 scale (grids/A): 1.759792 object centre (A): 3.903501 27.79400 26.08300 number of atom coordinates read : 3001 total number of charged atoms : 2859 net assigned charge : -2.485965 assigned positive charge : 457.6068 centred at (gu) : 90.67213 91.10613 88.62930 assigned negative charge : -460.0941 centred at (gu) : 90.96633 91.48802 88.39021 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 75309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28726 grid for indexing accessible points = 1.400000 m= 23831 mr = 50096 m= 2773 mr = 16332 m= 112 mr = 1414 m= 0 mr = 16 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 930 time to turn everything in is 0.6700000 number of dielectric boundary points 34167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 269 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 22237 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) : 0.5865972 object centre at (A) : 3.903501 27.79400 26.08300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5276736E-03 1.8714547E-02 midg,1,midg; midg,igrid,midg 6.0974630E-03 -1.8504588E-02 1,midg,midg; igrid,midg,midg 2.1570550E-02 -2.9804371E-02 gauss-seidel spectral radius is 0.9984574 estimated iterations to convergence 202 setup time was (sec) 0.9900000 now iterating at: 14:38:46 rms-change max change #iterations 4.007033 169.6612 at 10iterations 1.770917 70.51210 at 20iterations 0.7890502 24.56853 at 30iterations 0.3524855 11.39858 at 40iterations 0.1569044 5.071308 at 50iterations 7.0099466E-02 2.357162 at 60iterations 3.1129032E-02 1.015457 at 70iterations 1.3953971E-02 0.4555359 at 80iterations 6.2130759E-03 0.2080898 at 90iterations 2.7785888E-03 8.7196350E-02 at 100iterations 1.2360555E-03 4.2831421E-02 at 110iterations 5.5229105E-04 1.7608643E-02 at 120iterations finished qdiffx linear iterations at : 14:38:55 total time elapsed so far: 9.700000 # loops : 120 mean,max change (kT/e) : 5.5229105E-04 1.7608643E-02 energy calculations done at 9.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.890000 DelPhi exited at 14:38:56 9.890u 0.308s 0:10.68 95.4% 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 15 2011 at 14:38:56 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: HIT 107 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: 2.639688 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): -26.44100 34.24800 ymin,ymax (A): 3.908000 51.68000 zmin,zma (A): -3.453000 55.61900 x,y,z range (A): 60.68900 47.77200 59.07200 scale (grids/A): 2.639688 object centre (A): 3.903501 27.79400 26.08300 number of atom coordinates read : 3001 total number of charged atoms : 2859 net assigned charge : -2.485965 assigned positive charge : 457.6068 centred at (gu) : 91.00786 91.65908 87.94366 assigned negative charge : -460.0941 centred at (gu) : 91.44942 92.23183 87.58522 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 174549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28726 grid for indexing accessible points = 1.400000 m= 80582 mr = 122622 m= 24837 mr = 63380 m= 4456 mr = 18542 m= 386 mr = 2940 m= 12 mr = 189 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 3334 time to turn everything in is 1.650000 number of dielectric boundary points 77149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 22868 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) : 1.759792 object centre at (A) : 3.903501 27.79400 26.08300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1755562 0.2756718 midg,1,midg; midg,igrid,midg 7.1845584E-02 -0.2012874 1,midg,midg; igrid,midg,midg 0.3721023 -0.3425860 gauss-seidel spectral radius is 0.9992298 estimated iterations to convergence 284 setup time was (sec) 2.000000 now iterating at: 14:38:58 rms-change max change #iterations 9.983141 307.0768 at 10iterations 5.829805 150.7937 at 20iterations 3.351540 76.37897 at 30iterations 1.925644 44.08278 at 40iterations 1.107311 24.23372 at 50iterations 0.6319237 13.98363 at 60iterations 0.3608191 7.364784 at 70iterations 0.2053655 4.196562 at 80iterations 0.1173370 2.262489 at 90iterations 6.6635624E-02 1.271539 at 100iterations 3.7923425E-02 0.6863461 at 110iterations 2.1490689E-02 0.4238476 at 120iterations 1.2192685E-02 0.2194328 at 130iterations 6.9350903E-03 0.1274872 at 140iterations 3.9395522E-03 7.6961517E-02 at 150iterations 2.2378981E-03 4.1198730E-02 at 160iterations 1.2705079E-03 2.4501801E-02 at 170iterations 7.2045770E-04 1.4282227E-02 at 180iterations finished qdiffx linear iterations at : 14:39:12 total time elapsed so far: 16.47000 # loops : 180 mean,max change (kT/e) : 7.2045770E-04 1.4282227E-02 energy calculations done at 16.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.66000 DelPhi exited at 14:39:13 16.658u 0.340s 0:17.57 96.6% 0+0k 0+0io 0pf+0w