Mon Oct 10 17:11:23 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 Mon Oct 10 2011 at 17:11:23 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4626 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5086877 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): -15.94100 37.37100 ymin,ymax (A): -30.78600 34.49400 zmin,zma (A): -4.123000 65.86100 x,y,z range (A): 53.31200 65.28000 69.98400 scale (grids/A): 0.5086877 object centre (A): 10.71500 1.854002 30.86900 number of atom coordinates read : 4626 total number of charged atoms : 4381 net assigned charge : 6.800031 assigned positive charge : 692.0356 centred at (gu) : 89.44498 90.53139 88.05466 assigned negative charge : -685.2401 centred at (gu) : 89.36449 90.59941 88.03548 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7657 nv = 96 ne = 84 npr = 93004 no. pairs analyzed = 93004 no. exposed pairs = 5952 no. arc points = 41563 no. surface atoms = 1990 nbur = 2636 mkacc time = 0.2000000 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 = 1.680000 m= 272 mr = 3952 m= 0 mr = 10 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3984 ## 631 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.6965871E-11 8.1648327E-11 midg,1,midg; midg,igrid,midg 2.1289812E-10 -7.5938103E-11 1,midg,midg; igrid,midg,midg -1.1013670E-10 2.3559471E-10 gauss-seidel spectral radius is 0.9802294 estimated iterations to convergence 59 setup time was (sec) 0.6500000 now iterating at: 17:11:24 rms-change max change #iterations 6.5240577E-02 9.148819 at 10iterations 3.8062264E-03 0.5708981 at 20iterations 4.9302046E-04 6.7861557E-02 at 30iterations 1.8196231E-04 2.7256489E-02 at 40iterations 7.5184988E-05 1.1330128E-02 at 50iterations finished qdiffx linear iterations at : 17:11:26 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 7.5184988E-05 1.1330128E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 17:11:27 3.255u 0.150s 0:03.73 91.1% 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 Mon Oct 10 2011 at 17:11:27 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4626 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.526063 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): -15.94100 37.37100 ymin,ymax (A): -30.78600 34.49400 zmin,zma (A): -4.123000 65.86100 x,y,z range (A): 53.31200 65.28000 69.98400 scale (grids/A): 1.526063 object centre (A): 10.71500 1.854002 30.86900 number of atom coordinates read : 4626 total number of charged atoms : 4381 net assigned charge : 6.800031 assigned positive charge : 692.0356 centred at (gu) : 88.33356 91.59325 84.16290 assigned negative charge : -685.2401 centred at (gu) : 88.09319 91.79811 84.10642 start vw surface at 0.2000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 86401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41563 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 24800 mr = 59010 m= 2177 mr = 16362 m= 41 mr = 885 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 37159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 562 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 32970 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) : 0.5086877 object centre at (A) : 10.71500 1.854002 30.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5097173E-03 1.8158289E-02 midg,1,midg; midg,igrid,midg 4.2075189E-03 -1.2199852E-02 1,midg,midg; igrid,midg,midg 5.4311205E-04 8.9956606E-03 gauss-seidel spectral radius is 0.9980860 estimated iterations to convergence 182 setup time was (sec) 0.8600000 now iterating at: 17:11:28 rms-change max change #iterations 3.687164 156.2731 at 10iterations 1.498624 57.14296 at 20iterations 0.6136954 19.67034 at 30iterations 0.2500111 8.570242 at 40iterations 0.1017737 3.541925 at 50iterations 4.1662522E-02 1.383795 at 60iterations 1.7037963E-02 0.5538177 at 70iterations 7.0222802E-03 0.2561073 at 80iterations 2.9363714E-03 9.9245071E-02 at 90iterations 1.2682340E-03 4.0823221E-02 at 100iterations 6.0219830E-04 2.0483971E-02 at 110iterations 3.2860326E-04 1.1550426E-02 at 120iterations finished qdiffx linear iterations at : 17:11:34 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 3.2860326E-04 1.1550426E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 17:11:34 6.954u 0.173s 0:07.58 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 Mon Oct 10 2011 at 17:11:34 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4626 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.289095 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): -15.94100 37.37100 ymin,ymax (A): -30.78600 34.49400 zmin,zma (A): -4.123000 65.86100 x,y,z range (A): 53.31200 65.28000 69.98400 scale (grids/A): 2.289095 object centre (A): 10.71500 1.854002 30.86900 number of atom coordinates read : 4626 total number of charged atoms : 4381 net assigned charge : 6.800031 assigned positive charge : 692.0356 centred at (gu) : 87.50000 92.38937 81.24403 assigned negative charge : -685.2401 centred at (gu) : 87.13979 92.69705 81.15966 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 201272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41563 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 89381 mr = 144926 m= 22216 mr = 69686 m= 3047 mr = 15677 m= 145 mr = 1805 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.440000 number of dielectric boundary points 83917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 34957 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) : 1.526063 object centre at (A) : 10.71500 1.854002 30.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1257798 0.4448857 midg,1,midg; midg,igrid,midg 3.6304411E-02 -0.2794764 1,midg,midg; igrid,midg,midg 1.2397581E-03 0.1409726 gauss-seidel spectral radius is 0.9991522 estimated iterations to convergence 271 setup time was (sec) 1.760000 now iterating at: 17:11:36 rms-change max change #iterations 9.990191 255.9542 at 10iterations 5.699217 130.3426 at 20iterations 3.224796 76.51547 at 30iterations 1.817003 51.37771 at 40iterations 1.020577 21.97309 at 50iterations 0.5714387 12.27809 at 60iterations 0.3188111 6.886505 at 70iterations 0.1773921 3.805021 at 80iterations 9.8637141E-02 2.178574 at 90iterations 5.4913059E-02 1.053717 at 100iterations 3.0478789E-02 0.6073370 at 110iterations 1.6921235E-02 0.3470898 at 120iterations 9.3707442E-03 0.1956034 at 130iterations 5.2036596E-03 9.9221647E-02 at 140iterations 2.8883121E-03 6.2379837E-02 at 150iterations 1.6076363E-03 3.4641266E-02 at 160iterations 8.9797314E-04 1.7044067E-02 at 170iterations 5.0646445E-04 1.0249615E-02 at 180iterations finished qdiffx linear iterations at : 17:11:48 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 5.0646445E-04 1.0249615E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.61000 DelPhi exited at 17:11:49 13.612u 0.301s 0:14.30 97.2% 0+0k 0+0io 0pf+0w