Sun Oct 9 00:54:57 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 Sun Oct 9 2011 at 00:54:58 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2324 !!! WARNING: HIT 84 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: 0.6393679 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): -0.1380000 53.44200 ymin,ymax (A): -15.67100 27.52600 zmin,zma (A): 28.71500 84.39500 x,y,z range (A): 53.58000 43.19700 55.68000 scale (grids/A): 0.6393679 object centre (A): 26.65200 5.927501 56.55500 number of atom coordinates read : 2324 total number of charged atoms : 2189 net assigned charge : 9.014025 assigned positive charge : 339.0234 centred at (gu) : 90.45154 89.05885 89.24226 assigned negative charge : -330.0102 centred at (gu) : 90.41374 89.23042 89.23406 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6420 nv = 96 ne = 84 npr = 46632 no. pairs analyzed = 46632 no. exposed pairs = 3132 no. arc points = 22500 no. surface atoms = 1046 nbur = 1278 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3225 m= 6 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2199 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7698 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3913089E-08 1.1540521E-08 midg,1,midg; midg,igrid,midg 3.5603236E-08 -3.4123306E-09 1,midg,midg; igrid,midg,midg 8.2179525E-09 1.7987611E-08 gauss-seidel spectral radius is 0.9873111 estimated iterations to convergence 73 setup time was (sec) 0.4800000 now iterating at: 00:54:58 rms-change max change #iterations 0.1355046 23.22613 at 10iterations 1.3183881E-02 1.881477 at 20iterations 1.3247638E-03 0.2080078 at 30iterations 1.3243234E-04 1.8001556E-02 at 40iterations 1.5217488E-05 2.1228790E-03 at 50iterations finished qdiffx linear iterations at : 00:55:01 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 1.5217488E-05 2.1228790E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 00:55:01 3.276u 0.136s 0:03.69 92.1% 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 Sun Oct 9 2011 at 00:55:01 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2324 !!! WARNING: HIT 84 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.918104 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): -0.1380000 53.44200 ymin,ymax (A): -15.67100 27.52600 zmin,zma (A): 28.71500 84.39500 x,y,z range (A): 53.58000 43.19700 55.68000 scale (grids/A): 1.918104 object centre (A): 26.65200 5.927501 56.55500 number of atom coordinates read : 2324 total number of charged atoms : 2189 net assigned charge : 9.014025 assigned positive charge : 339.0234 centred at (gu) : 91.35425 87.17637 87.72663 assigned negative charge : -330.0102 centred at (gu) : 91.24139 87.69136 87.70226 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22500 grid for indexing accessible points = 1.400000 m= 24019 mr = 45417 m= 3938 mr = 16721 m= 306 mr = 2270 m= 5 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 32756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 17227 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) : 0.6393679 object centre at (A) : 26.65200 5.927501 56.55500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1019634E-02 4.1503739E-02 midg,1,midg; midg,igrid,midg 3.0809831E-02 -1.4147089E-02 1,midg,midg; igrid,midg,midg 3.9603703E-02 5.2076951E-02 gauss-seidel spectral radius is 0.9986370 estimated iterations to convergence 215 setup time was (sec) 0.7900000 now iterating at: 00:55:02 rms-change max change #iterations 3.989041 173.2740 at 10iterations 1.864167 66.02785 at 20iterations 0.8708085 30.07276 at 30iterations 0.4072960 13.73484 at 40iterations 0.1906870 6.953655 at 50iterations 8.9068107E-02 3.127260 at 60iterations 4.1799534E-02 1.418525 at 70iterations 1.9540237E-02 0.6459408 at 80iterations 9.1228019E-03 0.2903337 at 90iterations 4.2844187E-03 0.1442432 at 100iterations 2.0035591E-03 6.8521500E-02 at 110iterations 9.3748147E-04 3.0651093E-02 at 120iterations finished qdiffx linear iterations at : 00:55:08 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 9.3748147E-04 3.0651093E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 00:55:09 6.890u 0.165s 0:07.34 96.0% 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 Sun Oct 9 2011 at 00:55:09 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2324 !!! WARNING: HIT 84 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.877155 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): -0.1380000 53.44200 ymin,ymax (A): -15.67100 27.52600 zmin,zma (A): 28.71500 84.39500 x,y,z range (A): 53.58000 43.19700 55.68000 scale (grids/A): 2.877155 object centre (A): 26.65200 5.927501 56.55500 number of atom coordinates read : 2324 total number of charged atoms : 2189 net assigned charge : 9.014025 assigned positive charge : 339.0234 centred at (gu) : 92.03120 85.76450 86.58979 assigned negative charge : -330.0102 centred at (gu) : 91.86214 86.53707 86.55347 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 159199 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22500 grid for indexing accessible points = 1.400000 m= 76980 mr = 110750 m= 27996 mr = 60636 m= 7108 mr = 21674 m= 1256 mr = 5022 m= 74 mr = 762 m= 0 mr = 11 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.210000 number of dielectric boundary points 73758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 17512 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) : 1.918104 object centre at (A) : 26.65200 5.927501 56.55500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2969413 0.6084869 midg,1,midg; midg,igrid,midg 0.3009957 -0.1468144 1,midg,midg; igrid,midg,midg 0.4525342 0.5223959 gauss-seidel spectral radius is 0.9992673 estimated iterations to convergence 292 setup time was (sec) 1.490000 now iterating at: 00:55:10 rms-change max change #iterations 9.428285 339.5281 at 10iterations 5.566074 140.2752 at 20iterations 3.253905 72.93492 at 30iterations 1.900482 40.26672 at 40iterations 1.107265 24.75660 at 50iterations 0.6414264 12.17211 at 60iterations 0.3718536 7.235997 at 70iterations 0.2152810 3.980033 at 80iterations 0.1244779 2.501266 at 90iterations 7.1954131E-02 1.292595 at 100iterations 4.1530754E-02 0.7576327 at 110iterations 2.4005307E-02 0.4684842 at 120iterations 1.3816499E-02 0.2605762 at 130iterations 7.9672178E-03 0.1608403 at 140iterations 4.5956750E-03 8.4591746E-02 at 150iterations 2.6487706E-03 5.2452087E-02 at 160iterations 1.5266050E-03 2.7540207E-02 at 170iterations 8.8263914E-04 1.6574860E-02 at 180iterations finished qdiffx linear iterations at : 00:55:20 total time elapsed so far: 10.86000 # loops : 180 mean,max change (kT/e) : 8.8263914E-04 1.6574860E-02 energy calculations done at 10.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.03000 DelPhi exited at 00:55:20 11.034u 0.220s 0:11.53 97.5% 0+0k 0+0io 0pf+0w