Sun Oct 9 07:24:56 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 07:24:56 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1683 !!! WARNING: NAP 164 has a net charge of -2.3370 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: 0.7283888 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): -7.407000 34.70200 ymin,ymax (A): -2.452000 40.09200 zmin,zma (A): -13.21700 35.65800 x,y,z range (A): 42.10900 42.54400 48.87500 scale (grids/A): 0.7283888 object centre (A): 13.64750 18.82000 11.22050 number of atom coordinates read : 1683 total number of charged atoms : 1546 net assigned charge : -11.83699 assigned positive charge : 249.1672 centred at (gu) : 91.05938 89.53906 90.21478 assigned negative charge : -261.0041 centred at (gu) : 90.90804 89.90199 90.32522 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6183 nv = 96 ne = 84 npr = 35322 no. pairs analyzed = 35322 no. exposed pairs = 2081 no. arc points = 14926 no. surface atoms = 709 nbur = 974 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 3531 m= 2 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 150 time to turn everything in is 0.2400000 number of dielectric boundary points 3000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1201 ## 66 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6499 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8561272E-08 -2.4538579E-07 midg,1,midg; midg,igrid,midg 7.2130028E-08 -3.7374028E-07 1,midg,midg; igrid,midg,midg -2.1594950E-07 -7.8687975E-08 gauss-seidel spectral radius is 0.9901378 estimated iterations to convergence 82 setup time was (sec) 0.4600000 now iterating at: 07:24:57 rms-change max change #iterations 0.2052954 27.17483 at 10iterations 2.7808119E-02 4.292891 at 20iterations 3.5662977E-03 0.4773498 at 30iterations 4.5855911E-04 7.1147919E-02 at 40iterations 6.0490311E-05 9.0365410E-03 at 50iterations finished qdiffx linear iterations at : 07:24:59 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 6.0490311E-05 9.0365410E-03 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 07:25:00 3.046u 0.146s 0:03.49 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 Sun Oct 9 2011 at 07:25:00 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1683 !!! WARNING: NAP 164 has a net charge of -2.3370 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: 2.185166 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): -7.407000 34.70200 ymin,ymax (A): -2.452000 40.09200 zmin,zma (A): -13.21700 35.65800 x,y,z range (A): 42.10900 42.54400 48.87500 scale (grids/A): 2.185166 object centre (A): 13.64750 18.82000 11.22050 number of atom coordinates read : 1683 total number of charged atoms : 1546 net assigned charge : -11.83699 assigned positive charge : 249.1672 centred at (gu) : 93.17859 88.61716 90.64429 assigned negative charge : -261.0041 centred at (gu) : 92.72398 89.70607 90.97577 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 64838 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14926 grid for indexing accessible points = 1.400000 m= 26582 mr = 44942 m= 5462 mr = 20617 m= 597 mr = 3931 m= 26 mr = 379 m= 0 mr = 7 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3967 time to turn everything in is 0.4700000 number of dielectric boundary points 27629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 12321 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) : 0.7283888 object centre at (A) : 13.64750 18.82000 11.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6171839E-02 -8.1581622E-02 midg,1,midg; midg,igrid,midg 1.1224623E-02 -0.1065961 1,midg,midg; igrid,midg,midg -6.7549005E-02 -2.5607215E-02 gauss-seidel spectral radius is 0.9988555 estimated iterations to convergence 234 setup time was (sec) 0.7200000 now iterating at: 07:25:01 rms-change max change #iterations 4.460417 196.3356 at 10iterations 2.210658 83.72938 at 20iterations 1.109391 34.99429 at 30iterations 0.5499067 16.83250 at 40iterations 0.2755810 8.465643 at 50iterations 0.1375048 4.430016 at 60iterations 6.8485387E-02 2.136578 at 70iterations 3.4185089E-02 1.115340 at 80iterations 1.7091027E-02 0.5671091 at 90iterations 8.4940223E-03 0.2615719 at 100iterations 4.2586676E-03 0.1465149 at 110iterations 2.1271729E-03 7.1752548E-02 at 120iterations finished qdiffx linear iterations at : 07:25:07 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 2.1271729E-03 7.1752548E-02 energy calculations done at 6.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 07:25:07 6.815u 0.163s 0:07.27 95.8% 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 07:25:07 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1683 !!! WARNING: NAP 164 has a net charge of -2.3370 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: 3.277750 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): -7.407000 34.70200 ymin,ymax (A): -2.452000 40.09200 zmin,zma (A): -13.21700 35.65800 x,y,z range (A): 42.10900 42.54400 48.87500 scale (grids/A): 3.277750 object centre (A): 13.64750 18.82000 11.22050 number of atom coordinates read : 1683 total number of charged atoms : 1546 net assigned charge : -11.83699 assigned positive charge : 249.1672 centred at (gu) : 94.76785 87.92584 90.96638 assigned negative charge : -261.0041 centred at (gu) : 94.08602 89.55911 91.46371 start vw surface at 0.1200000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 149098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14926 grid for indexing accessible points = 1.400000 m= 80848 mr = 107679 m= 35302 mr = 67956 m= 10671 mr = 30002 m= 2319 mr = 8566 m= 380 mr = 1820 m= 26 mr = 310 m= 0 mr = 11 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 13617 time to turn everything in is 1.500000 number of dielectric boundary points 62300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 12368 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) : 2.185166 object centre at (A) : 13.64750 18.82000 11.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1311957 -0.7164563 midg,1,midg; midg,igrid,midg 0.1486810 -0.7405896 1,midg,midg; igrid,midg,midg -0.4980205 -0.1667761 gauss-seidel spectral radius is 0.9992935 estimated iterations to convergence 297 setup time was (sec) 1.770000 now iterating at: 07:25:09 rms-change max change #iterations 9.779572 400.1381 at 10iterations 5.672520 142.0277 at 20iterations 3.303859 68.72673 at 30iterations 1.923086 38.37039 at 40iterations 1.116776 23.69102 at 50iterations 0.6493496 11.63019 at 60iterations 0.3776021 7.115491 at 70iterations 0.2195263 4.127611 at 80iterations 0.1269869 2.360191 at 90iterations 7.4006304E-02 1.364363 at 100iterations 4.2992212E-02 0.8346705 at 110iterations 2.4975330E-02 0.4500198 at 120iterations 1.4536622E-02 0.2702742 at 130iterations 8.4312810E-03 0.1477537 at 140iterations 4.8951544E-03 9.0469360E-02 at 150iterations 2.8467374E-03 4.9370170E-02 at 160iterations 1.6570495E-03 2.8369904E-02 at 170iterations 9.6247304E-04 1.7242432E-02 at 180iterations finished qdiffx linear iterations at : 07:25:18 total time elapsed so far: 10.99000 # loops : 180 mean,max change (kT/e) : 9.6247304E-04 1.7242432E-02 energy calculations done at 10.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.16000 DelPhi exited at 07:25:19 11.161u 0.152s 0:11.57 97.7% 0+0k 0+0io 0pf+0w