Tue Oct 11 06:11:17 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 Tue Oct 11 2011 at 06:11:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2024 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: 0.7233126 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): -19.43100 23.86100 ymin,ymax (A): 0.7210001 39.09500 zmin,zma (A): 20.46000 69.67800 x,y,z range (A): 43.29200 38.37400 49.21800 scale (grids/A): 0.7233126 object centre (A): 2.215000 19.90800 45.06900 number of atom coordinates read : 2024 total number of charged atoms : 1901 net assigned charge : 7.500009 assigned positive charge : 306.8221 centred at (gu) : 89.94855 90.95203 89.81107 assigned negative charge : -299.3222 centred at (gu) : 89.75511 90.93671 89.77544 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7309 nv = 96 ne = 84 npr = 40754 no. pairs analyzed = 40754 no. exposed pairs = 2479 no. arc points = 16798 no. surface atoms = 845 nbur = 1179 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 497 mr = 4224 m= 4 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1555 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7853 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9817879E-08 1.1128202E-07 midg,1,midg; midg,igrid,midg 6.8291101E-08 1.2145119E-07 1,midg,midg; igrid,midg,midg -4.1188120E-08 2.1658326E-07 gauss-seidel spectral radius is 0.9900266 estimated iterations to convergence 81 setup time was (sec) 0.6200000 now iterating at: 06:11:18 rms-change max change #iterations 0.2108307 27.99404 at 10iterations 2.7475098E-02 3.249226 at 20iterations 3.7199974E-03 0.4561424 at 30iterations 5.6915462E-04 7.1998596E-02 at 40iterations 1.1700377E-04 1.4308929E-02 at 50iterations finished qdiffx linear iterations at : 06:11:22 total time elapsed so far: 4.410000 # loops : 50 mean,max change (kT/e) : 1.1700377E-04 1.4308929E-02 energy calculations done at 4.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 06:11:23 4.630u 0.454s 0:05.66 89.7% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 06:11:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2024 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: 2.169938 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): -19.43100 23.86100 ymin,ymax (A): 0.7210001 39.09500 zmin,zma (A): 20.46000 69.67800 x,y,z range (A): 43.29200 38.37400 49.21800 scale (grids/A): 2.169938 object centre (A): 2.215000 19.90800 45.06900 number of atom coordinates read : 2024 total number of charged atoms : 1901 net assigned charge : 7.500009 assigned positive charge : 306.8221 centred at (gu) : 89.84568 92.85637 89.43301 assigned negative charge : -299.3222 centred at (gu) : 89.26539 92.81017 89.32642 start vw surface at 0.1400000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 76616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16798 grid for indexing accessible points = 1.400000 m= 32165 mr = 54736 m= 6760 mr = 24699 m= 643 mr = 4579 m= 15 mr = 343 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 31842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 15109 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) : 0.7233126 object centre at (A) : 2.215000 19.90800 45.06900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1011347E-02 5.8186453E-02 midg,1,midg; midg,igrid,midg 5.2408995E-03 3.6982067E-02 1,midg,midg; igrid,midg,midg 1.1469275E-02 5.0967958E-02 gauss-seidel spectral radius is 0.9988688 estimated iterations to convergence 235 setup time was (sec) 1.160000 now iterating at: 06:11:24 rms-change max change #iterations 4.675065 200.3763 at 10iterations 2.334583 74.13648 at 20iterations 1.181458 39.55995 at 30iterations 0.5922471 18.07434 at 40iterations 0.2969278 9.486672 at 50iterations 0.1502928 4.573658 at 60iterations 7.5323127E-02 2.165665 at 70iterations 3.7915748E-02 1.202770 at 80iterations 1.9111136E-02 0.5503755 at 90iterations 9.6337488E-03 0.2909179 at 100iterations 4.8710285E-03 0.1347389 at 110iterations 2.4772335E-03 7.4287415E-02 at 120iterations finished qdiffx linear iterations at : 06:11:34 total time elapsed so far: 10.97000 # loops : 120 mean,max change (kT/e) : 2.4772335E-03 7.4287415E-02 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.20000 DelPhi exited at 06:11:35 11.207u 0.474s 0:12.12 96.2% 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 Tue Oct 11 2011 at 06:11:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2024 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: 3.254907 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): -19.43100 23.86100 ymin,ymax (A): 0.7210001 39.09500 zmin,zma (A): 20.46000 69.67800 x,y,z range (A): 43.29200 38.37400 49.21800 scale (grids/A): 3.254907 object centre (A): 2.215000 19.90800 45.06900 number of atom coordinates read : 2024 total number of charged atoms : 1901 net assigned charge : 7.500009 assigned positive charge : 306.8221 centred at (gu) : 89.76851 94.28461 89.14954 assigned negative charge : -299.3222 centred at (gu) : 88.89819 94.21520 88.98969 start vw surface at 0.1300000 fill in re-entrant regions at 1.010000 boundary points on vw surface= 176299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16798 grid for indexing accessible points = 1.400000 m= 98770 mr = 131685 m= 42540 mr = 82656 m= 12945 mr = 35177 m= 2622 mr = 10128 m= 313 mr = 1919 m= 5 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.540000 number of dielectric boundary points 71725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.680000 number of grid points assigned charge 15204 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) : 2.169938 object centre at (A) : 2.215000 19.90800 45.06900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8285411 0.4559990 midg,1,midg; midg,igrid,midg 3.4691715E-03 0.2773013 1,midg,midg; igrid,midg,midg 0.1664408 0.3892356 gauss-seidel spectral radius is 0.9993030 estimated iterations to convergence 299 setup time was (sec) 2.900000 now iterating at: 06:11:38 rms-change max change #iterations 10.36769 321.7995 at 10iterations 6.155043 130.4034 at 20iterations 3.657043 75.99371 at 30iterations 2.164846 44.46468 at 40iterations 1.278384 24.48711 at 50iterations 0.7529684 14.31676 at 60iterations 0.4446183 7.650780 at 70iterations 0.2612369 4.929343 at 80iterations 0.1540510 2.670175 at 90iterations 9.0449251E-02 1.646969 at 100iterations 5.3170744E-02 0.9201183 at 110iterations 3.1398360E-02 0.5349274 at 120iterations 1.8584566E-02 0.3194656 at 130iterations 1.1152012E-02 0.1892881 at 140iterations 6.7929956E-03 0.1234245 at 150iterations 4.2714709E-03 7.8315735E-02 at 160iterations 2.8152438E-03 5.3070068E-02 at 170iterations 1.9736520E-03 3.4202576E-02 at 180iterations finished qdiffx linear iterations at : 06:11:56 total time elapsed so far: 20.17000 # loops : 180 mean,max change (kT/e) : 1.9736520E-03 3.4202576E-02 energy calculations done at 20.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.38000 DelPhi exited at 06:11:56 20.380u 0.554s 0:21.50 97.3% 0+0k 0+0io 0pf+0w