Sat Oct 8 20:25:01 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 8 2011 at 20:25:01 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6258900 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): -38.69800 10.06200 ymin,ymax (A): -13.99000 33.58300 zmin,zma (A): -44.65500 12.22400 x,y,z range (A): 48.76000 47.57300 56.87900 scale (grids/A): 0.6258900 object centre (A): -14.31800 9.796500 -16.21550 number of atom coordinates read : 2579 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 393.7700 centred at (gu) : 91.57839 89.44486 90.28859 assigned negative charge : -390.3226 centred at (gu) : 91.67547 89.47275 90.37926 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6593 nv = 96 ne = 84 npr = 54128 no. pairs analyzed = 54128 no. exposed pairs = 2962 no. arc points = 21264 no. surface atoms = 990 nbur = 1589 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3711 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 85 time to turn everything in is 0.2000000 number of dielectric boundary points 3170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2154 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8199 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9017097E-09 -4.0312091E-09 midg,1,midg; midg,igrid,midg 6.3776997E-09 1.1271443E-09 1,midg,midg; igrid,midg,midg 7.8398879E-09 -6.2023506E-09 gauss-seidel spectral radius is 0.9867715 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 20:25:02 rms-change max change #iterations 0.1330993 20.45369 at 10iterations 1.2508383E-02 1.924537 at 20iterations 1.1979318E-03 0.2049481 at 30iterations 1.1271450E-04 1.5999794E-02 at 40iterations 1.0685731E-05 1.5563965E-03 at 50iterations finished qdiffx linear iterations at : 20:25:05 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 1.0685731E-05 1.5563965E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 20:25:05 3.663u 0.224s 0:04.17 93.0% 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 Sat Oct 8 2011 at 20:25:05 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.877670 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): -38.69800 10.06200 ymin,ymax (A): -13.99000 33.58300 zmin,zma (A): -44.65500 12.22400 x,y,z range (A): 48.76000 47.57300 56.87900 scale (grids/A): 1.877670 object centre (A): -14.31800 9.796500 -16.21550 number of atom coordinates read : 2579 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 393.7700 centred at (gu) : 94.73440 88.33402 90.86527 assigned negative charge : -390.3226 centred at (gu) : 95.02612 88.41817 91.13777 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21264 grid for indexing accessible points = 1.400000 m= 24458 mr = 50425 m= 3516 mr = 18168 m= 166 mr = 2237 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 6537 time to turn everything in is 0.3600000 number of dielectric boundary points 29081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19253 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) : 0.6258900 object centre at (A) : -14.31800 9.796500 -16.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7077701E-02 -5.2808677E-03 midg,1,midg; midg,igrid,midg 1.0363382E-02 -6.0890139E-05 1,midg,midg; igrid,midg,midg 3.7276365E-02 -5.6456714E-03 gauss-seidel spectral radius is 0.9985899 estimated iterations to convergence 211 setup time was (sec) 0.6100000 now iterating at: 20:25:06 rms-change max change #iterations 4.126121 167.4664 at 10iterations 1.899586 68.40646 at 20iterations 0.8791968 28.41161 at 30iterations 0.4063506 13.67787 at 40iterations 0.1889258 7.016638 at 50iterations 8.7161973E-02 2.702896 at 60iterations 4.0319987E-02 1.274516 at 70iterations 1.8737050E-02 0.5658312 at 80iterations 8.6473543E-03 0.2719313 at 90iterations 4.0033734E-03 0.1316013 at 100iterations 1.8502999E-03 6.1436653E-02 at 110iterations 8.5812144E-04 2.6802063E-02 at 120iterations finished qdiffx linear iterations at : 20:25:14 total time elapsed so far: 8.430000 # loops : 120 mean,max change (kT/e) : 8.5812144E-04 2.6802063E-02 energy calculations done at 8.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.560000 DelPhi exited at 20:25:14 8.567u 0.240s 0:09.13 96.3% 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 8 2011 at 20:25:14 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.816505 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): -38.69800 10.06200 ymin,ymax (A): -13.99000 33.58300 zmin,zma (A): -44.65500 12.22400 x,y,z range (A): 48.76000 47.57300 56.87900 scale (grids/A): 2.816505 object centre (A): -14.31800 9.796500 -16.21550 number of atom coordinates read : 2579 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 393.7700 centred at (gu) : 97.10146 87.50090 91.29781 assigned negative charge : -390.3226 centred at (gu) : 97.53904 87.62720 91.70647 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 166052 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21264 grid for indexing accessible points = 1.400000 m= 81641 mr = 121780 m= 27587 mr = 67358 m= 6322 mr = 22198 m= 812 mr = 4894 m= 29 mr = 544 m= 0 mr = 5 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 22423 time to turn everything in is 0.9500000 number of dielectric boundary points 65664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 19591 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) : 1.877670 object centre at (A) : -14.31800 9.796500 -16.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1170445 8.2551703E-02 midg,1,midg; midg,igrid,midg 0.1308719 -1.5359474E-02 1,midg,midg; igrid,midg,midg 0.4759156 -5.7981111E-02 gauss-seidel spectral radius is 0.9992381 estimated iterations to convergence 286 setup time was (sec) 1.220000 now iterating at: 20:25:16 rms-change max change #iterations 9.580997 347.3290 at 10iterations 5.476486 111.6948 at 20iterations 3.111726 61.95783 at 30iterations 1.767973 32.93422 at 40iterations 1.005449 17.52500 at 50iterations 0.5702627 10.71843 at 60iterations 0.3246694 6.740777 at 70iterations 0.1846891 3.896276 at 80iterations 0.1050168 2.076286 at 90iterations 5.9748627E-02 1.068890 at 100iterations 3.3912510E-02 0.6048393 at 110iterations 1.9300759E-02 0.3677673 at 120iterations 1.0968111E-02 0.2059746 at 130iterations 6.2479391E-03 0.1140099 at 140iterations 3.5490242E-03 6.1708450E-02 at 150iterations 2.0169707E-03 3.5808563E-02 at 160iterations 1.1496972E-03 2.0682335E-02 at 170iterations 6.5396400E-04 1.1800766E-02 at 180iterations finished qdiffx linear iterations at : 20:25:29 total time elapsed so far: 14.27000 # loops : 180 mean,max change (kT/e) : 6.5396400E-04 1.1800766E-02 energy calculations done at 14.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.40000 DelPhi exited at 20:25:29 14.406u 0.288s 0:15.02 97.7% 0+0k 0+0io 0pf+0w