Sun Oct 9 14:59:28 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 Sun Oct 9 2011 at 14:59:28 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 = 1424 !!! WARNING: GLU 107 has a net charge of -2.0000 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: 0.7295979 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): -6.391000 33.97100 ymin,ymax (A): -61.10900 -12.83800 zmin,zma (A): -29.42000 19.37400 x,y,z range (A): 40.36200 48.27100 48.79400 scale (grids/A): 0.7295979 object centre (A): 13.79000 -36.97350 -5.023000 number of atom coordinates read : 1424 total number of charged atoms : 1295 net assigned charge : 1.500007 assigned positive charge : 205.1544 centred at (gu) : 89.94984 91.25497 89.34299 assigned negative charge : -203.6543 centred at (gu) : 90.09206 91.14867 89.41312 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5376 nv = 96 ne = 84 npr = 28046 no. pairs analyzed = 28046 no. exposed pairs = 2069 no. arc points = 14421 no. surface atoms = 687 nbur = 737 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 2678 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 7.9999983E-02 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.2400000 number of dielectric boundary points 3035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1146 ## 78 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 5429 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3801565E-08 -1.4599252E-08 midg,1,midg; midg,igrid,midg -2.7930815E-08 9.5242420E-08 1,midg,midg; igrid,midg,midg 9.3954895E-08 -5.4514519E-08 gauss-seidel spectral radius is 0.9901506 estimated iterations to convergence 82 setup time was (sec) 0.4900000 now iterating at: 14:59:29 rms-change max change #iterations 0.1841979 36.29850 at 10iterations 2.3111371E-02 3.480607 at 20iterations 3.0141247E-03 0.4685926 at 30iterations 3.8928291E-04 7.1136475E-02 at 40iterations 4.9236445E-05 7.3394775E-03 at 50iterations finished qdiffx linear iterations at : 14:59:31 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 4.9236445E-05 7.3394775E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 14:59:32 3.517u 0.204s 0:03.99 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 Sun Oct 9 2011 at 14:59:32 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 = 1424 !!! WARNING: GLU 107 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.188794 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): -6.391000 33.97100 ymin,ymax (A): -61.10900 -12.83800 zmin,zma (A): -29.42000 19.37400 x,y,z range (A): 40.36200 48.27100 48.79400 scale (grids/A): 2.188794 object centre (A): 13.79000 -36.97350 -5.023000 number of atom coordinates read : 1424 total number of charged atoms : 1295 net assigned charge : 1.500007 assigned positive charge : 205.1544 centred at (gu) : 89.84983 93.76524 88.02921 assigned negative charge : -203.6543 centred at (gu) : 90.27645 93.44601 88.23951 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 56077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14421 grid for indexing accessible points = 1.400000 m= 21722 mr = 36358 m= 4123 mr = 15518 m= 366 mr = 2506 m= 14 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1200 time to turn everything in is 0.4900000 number of dielectric boundary points 27808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 10310 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) : 0.7295979 object centre at (A) : 13.79000 -36.97350 -5.023000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3279080E-02 1.5631733E-02 midg,1,midg; midg,igrid,midg -7.8263432E-03 2.7133912E-02 1,midg,midg; igrid,midg,midg 1.8800670E-02 -4.2351056E-03 gauss-seidel spectral radius is 0.9988459 estimated iterations to convergence 233 setup time was (sec) 0.7800000 now iterating at: 14:59:33 rms-change max change #iterations 3.895724 190.5229 at 10iterations 1.939655 76.41149 at 20iterations 0.9644678 35.79804 at 30iterations 0.4816172 17.30758 at 40iterations 0.2397333 8.843400 at 50iterations 0.1190126 4.861556 at 60iterations 5.9359688E-02 1.936717 at 70iterations 2.9575950E-02 1.071619 at 80iterations 1.4704061E-02 0.4985046 at 90iterations 7.2874953E-03 0.2455482 at 100iterations 3.6181908E-03 0.1248817 at 110iterations 1.8035542E-03 5.9914440E-02 at 120iterations finished qdiffx linear iterations at : 14:59:39 total time elapsed so far: 7.140000 # loops : 120 mean,max change (kT/e) : 1.8035542E-03 5.9914440E-02 energy calculations done at 7.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 14:59:40 7.333u 0.149s 0:07.81 95.6% 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 Sun Oct 9 2011 at 14:59:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1424 !!! WARNING: GLU 107 has a net charge of -2.0000 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: 3.283191 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): -6.391000 33.97100 ymin,ymax (A): -61.10900 -12.83800 zmin,zma (A): -29.42000 19.37400 x,y,z range (A): 40.36200 48.27100 48.79400 scale (grids/A): 3.283191 object centre (A): 13.79000 -36.97350 -5.023000 number of atom coordinates read : 1424 total number of charged atoms : 1295 net assigned charge : 1.500007 assigned positive charge : 205.1544 centred at (gu) : 89.77481 95.64790 87.04404 assigned negative charge : -203.6543 centred at (gu) : 90.41467 95.16914 87.35937 start vw surface at 0.1200000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 128879 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14421 grid for indexing accessible points = 1.400000 m= 66596 mr = 87933 m= 27071 mr = 53389 m= 7382 mr = 21231 m= 1371 mr = 5352 m= 129 mr = 777 m= 7 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 4066 time to turn everything in is 1.430000 number of dielectric boundary points 62702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 10360 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) : 2.188794 object centre at (A) : 13.79000 -36.97350 -5.023000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7753991E-02 0.2873336 midg,1,midg; midg,igrid,midg -2.9081564E-02 4.5972545E-02 1,midg,midg; igrid,midg,midg 0.1488834 -4.2995274E-02 gauss-seidel spectral radius is 0.9993062 estimated iterations to convergence 300 setup time was (sec) 1.720000 now iterating at: 14:59:42 rms-change max change #iterations 8.757244 337.4270 at 10iterations 5.260253 221.0699 at 20iterations 3.129994 73.86421 at 30iterations 1.854595 44.78506 at 40iterations 1.096537 26.02381 at 50iterations 0.6486579 15.25174 at 60iterations 0.3812163 7.883850 at 70iterations 0.2242482 4.848091 at 80iterations 0.1317519 3.109968 at 90iterations 7.7089332E-02 1.505312 at 100iterations 4.5165505E-02 0.9591866 at 110iterations 2.6507562E-02 0.5751648 at 120iterations 1.5496026E-02 0.3174286 at 130iterations 9.0331286E-03 0.2105865 at 140iterations 5.2864044E-03 0.1111498 at 150iterations 3.0855730E-03 6.0153961E-02 at 160iterations 1.8025917E-03 3.5827637E-02 at 170iterations 1.0541144E-03 2.0840645E-02 at 180iterations finished qdiffx linear iterations at : 14:59:52 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 1.0541144E-03 2.0840645E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 14:59:52 11.873u 0.187s 0:12.33 97.7% 0+0k 0+0io 0pf+0w