Wed Dec 28 11:06:35 PST 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 Wed Dec 28 2011 at 11:06:35 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 0.6099650 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): -23.86100 34.50300 ymin,ymax (A): -19.93600 20.62200 zmin,zma (A): -3.590000 38.67000 x,y,z range (A): 58.36400 40.55800 42.26000 scale (grids/A): 0.6099650 object centre (A): 5.321001 0.3430004 17.54000 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000004 assigned positive charge : 290.2520 centred at (gu) : 89.89139 90.57922 90.51297 assigned negative charge : -286.2523 centred at (gu) : 89.91200 90.71641 90.68431 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4939 nv = 96 ne = 84 npr = 40123 no. pairs analyzed = 40123 no. exposed pairs = 2545 no. arc points = 17678 no. surface atoms = 859 nbur = 1109 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 250 mr = 2677 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1795 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 5982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.6321918E-09 -4.4402531E-09 midg,1,midg; midg,igrid,midg 6.4660743E-09 -3.0378497E-09 1,midg,midg; igrid,midg,midg 3.2619245E-09 1.6441054E-09 gauss-seidel spectral radius is 0.9860313 estimated iterations to convergence 69 setup time was (sec) 0.4600000 now iterating at: 11:06:36 rms-change max change #iterations 9.9483185E-02 16.94141 at 10iterations 8.5773263E-03 1.678885 at 20iterations 7.5107499E-04 0.1257095 at 30iterations 6.7488021E-05 1.1545420E-02 at 40iterations 5.8968817E-06 9.8991394E-04 at 50iterations finished qdiffx linear iterations at : 11:06:38 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 5.8968817E-06 9.8991394E-04 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 11:06:39 3.031u 0.121s 0:03.46 91.0% 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 Wed Dec 28 2011 at 11:06:39 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 1.829895 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): -23.86100 34.50300 ymin,ymax (A): -19.93600 20.62200 zmin,zma (A): -3.590000 38.67000 x,y,z range (A): 58.36400 40.55800 42.26000 scale (grids/A): 1.829895 object centre (A): 5.321001 0.3430004 17.54000 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000004 assigned positive charge : 290.2520 centred at (gu) : 89.67423 91.73779 91.53875 assigned negative charge : -286.2523 centred at (gu) : 89.73630 92.14937 92.05290 start vw surface at 0.1700000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 53361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17678 grid for indexing accessible points = 1.400000 m= 19642 mr = 36515 m= 2922 mr = 14609 m= 130 mr = 1852 m= 0 mr = 18 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 23061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 14372 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) : 0.6099650 object centre at (A) : 5.321001 0.3430004 17.54000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7952606E-03 -8.1099058E-03 midg,1,midg; midg,igrid,midg 7.7621797E-03 -3.4872347E-03 1,midg,midg; igrid,midg,midg 3.8112402E-02 3.6769312E-02 gauss-seidel spectral radius is 0.9984465 estimated iterations to convergence 201 setup time was (sec) 0.6800000 now iterating at: 11:06:40 rms-change max change #iterations 3.311442 149.1335 at 10iterations 1.465953 58.22281 at 20iterations 0.6556629 23.63070 at 30iterations 0.2900800 11.86073 at 40iterations 0.1294528 4.590996 at 50iterations 5.7570741E-02 2.221555 at 60iterations 2.5536090E-02 1.072684 at 70iterations 1.1355715E-02 0.4265003 at 80iterations 5.0629894E-03 0.2089763 at 90iterations 2.2571075E-03 8.0822945E-02 at 100iterations 1.0030830E-03 3.8160086E-02 at 110iterations 4.4619138E-04 1.6826630E-02 at 120iterations finished qdiffx linear iterations at : 11:06:46 total time elapsed so far: 6.580000 # loops : 120 mean,max change (kT/e) : 4.4619138E-04 1.6826630E-02 energy calculations done at 6.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.760000 DelPhi exited at 11:06:46 6.765u 0.163s 0:07.27 95.1% 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 Wed Dec 28 2011 at 11:06:46 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 2.744843 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): -23.86100 34.50300 ymin,ymax (A): -19.93600 20.62200 zmin,zma (A): -3.590000 38.67000 x,y,z range (A): 58.36400 40.55800 42.26000 scale (grids/A): 2.744843 object centre (A): 5.321001 0.3430004 17.54000 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000004 assigned positive charge : 290.2520 centred at (gu) : 89.51144 92.60661 92.30816 assigned negative charge : -286.2523 centred at (gu) : 89.60452 93.22412 93.07936 start vw surface at 0.1300000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 123232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17678 grid for indexing accessible points = 1.400000 m= 63222 mr = 88333 m= 23219 mr = 52056 m= 5281 mr = 18855 m= 568 mr = 4012 m= 17 mr = 323 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 51960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 14683 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) : 1.829895 object centre at (A) : 5.321001 0.3430004 17.54000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3839784E-02 -7.9961360E-02 midg,1,midg; midg,igrid,midg 5.8622353E-02 -2.0638511E-02 1,midg,midg; igrid,midg,midg 0.3949158 0.4426663 gauss-seidel spectral radius is 0.9991908 estimated iterations to convergence 278 setup time was (sec) 1.210000 now iterating at: 11:06:48 rms-change max change #iterations 8.000927 312.3658 at 10iterations 4.570354 135.0792 at 20iterations 2.595321 69.83585 at 30iterations 1.467153 40.02557 at 40iterations 0.8268162 18.82342 at 50iterations 0.4644468 10.73837 at 60iterations 0.2603517 5.927083 at 70iterations 0.1463627 3.099188 at 80iterations 8.2057446E-02 1.748306 at 90iterations 4.6036396E-02 0.9724897 at 100iterations 2.5718005E-02 0.5820274 at 110iterations 1.4445787E-02 0.3142344 at 120iterations 8.0907913E-03 0.1728134 at 130iterations 4.5269690E-03 9.4631195E-02 at 140iterations 2.5306894E-03 5.4780960E-02 at 150iterations 1.4167133E-03 2.8945476E-02 at 160iterations 7.9230405E-04 1.8033981E-02 at 170iterations 4.4388528E-04 1.0175139E-02 at 180iterations finished qdiffx linear iterations at : 11:06:57 total time elapsed so far: 10.30000 # loops : 180 mean,max change (kT/e) : 4.4388528E-04 1.0175139E-02 energy calculations done at 10.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.48000 DelPhi exited at 11:06:57 10.482u 0.163s 0:10.98 96.9% 0+0k 0+0io 0pf+0w