Tue Oct 11 06:43:13 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 Tue Oct 11 2011 at 06:43:13 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2080 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7179157 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): -36.43400 9.380000 ymin,ymax (A): -3.716000 33.24000 zmin,zma (A): 20.27500 69.86300 x,y,z range (A): 45.81400 36.95600 49.58800 scale (grids/A): 0.7179157 object centre (A): -13.52700 14.76200 45.06900 number of atom coordinates read : 2080 total number of charged atoms : 1946 net assigned charge : 5.945010 assigned positive charge : 318.9280 centred at (gu) : 90.59830 89.59233 88.70956 assigned negative charge : -312.9831 centred at (gu) : 90.74454 89.61827 88.66307 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6860 nv = 96 ne = 84 npr = 43542 no. pairs analyzed = 43542 no. exposed pairs = 2396 no. arc points = 16427 no. surface atoms = 820 nbur = 1260 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 409 mr = 3921 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.1700000 number of dielectric boundary points 3285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1499 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7884 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5049138E-08 7.3619219E-08 midg,1,midg; midg,igrid,midg 8.7536989E-08 4.5270038E-08 1,midg,midg; igrid,midg,midg 1.3802405E-07 -3.1494800E-08 gauss-seidel spectral radius is 0.9898754 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 06:43:14 rms-change max change #iterations 0.2212462 35.44065 at 10iterations 2.8690085E-02 4.153694 at 20iterations 3.5730461E-03 0.5240364 at 30iterations 4.6960884E-04 6.3754082E-02 at 40iterations 6.2416322E-05 7.4048042E-03 at 50iterations finished qdiffx linear iterations at : 06:43:17 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 6.2416322E-05 7.4048042E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:43:17 3.343u 0.161s 0:03.81 91.8% 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 Tue Oct 11 2011 at 06:43:17 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2080 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.153747 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): -36.43400 9.380000 ymin,ymax (A): -3.716000 33.24000 zmin,zma (A): 20.27500 69.86300 x,y,z range (A): 45.81400 36.95600 49.58800 scale (grids/A): 2.153747 object centre (A): -13.52700 14.76200 45.06900 number of atom coordinates read : 2080 total number of charged atoms : 1946 net assigned charge : 5.945010 assigned positive charge : 318.9280 centred at (gu) : 91.79504 88.77714 86.12871 assigned negative charge : -312.9831 centred at (gu) : 92.23379 88.85483 85.98941 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16427 grid for indexing accessible points = 1.400000 m= 27202 mr = 52248 m= 4905 mr = 20176 m= 474 mr = 3167 m= 12 mr = 253 m= 0 mr = 6 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1679 time to turn everything in is 0.3700000 number of dielectric boundary points 30271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 15484 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) : 0.7179157 object centre at (A) : -13.52700 14.76200 45.06900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1504560E-02 5.8999877E-02 midg,1,midg; midg,igrid,midg 2.8794926E-02 1.0137305E-02 1,midg,midg; igrid,midg,midg 3.4896366E-02 1.3327509E-02 gauss-seidel spectral radius is 0.9988515 estimated iterations to convergence 234 setup time was (sec) 0.5600000 now iterating at: 06:43:18 rms-change max change #iterations 4.757599 172.6514 at 10iterations 2.358683 81.18194 at 20iterations 1.178611 37.10259 at 30iterations 0.5872108 20.67400 at 40iterations 0.2936124 9.947045 at 50iterations 0.1469683 4.246504 at 60iterations 7.3304139E-02 2.092667 at 70iterations 3.6451943E-02 1.243776 at 80iterations 1.8255096E-02 0.5883179 at 90iterations 9.1567123E-03 0.2768288 at 100iterations 4.5527392E-03 0.1407814 at 110iterations 2.2796935E-03 6.9731712E-02 at 120iterations finished qdiffx linear iterations at : 06:43:25 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 2.2796935E-03 6.9731712E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 06:43:26 7.683u 0.214s 0:08.44 93.4% 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 06:43:26 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2080 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.230620 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): -36.43400 9.380000 ymin,ymax (A): -3.716000 33.24000 zmin,zma (A): 20.27500 69.86300 x,y,z range (A): 45.81400 36.95600 49.58800 scale (grids/A): 3.230620 object centre (A): -13.52700 14.76200 45.06900 number of atom coordinates read : 2080 total number of charged atoms : 1946 net assigned charge : 5.945010 assigned positive charge : 318.9280 centred at (gu) : 92.69231 88.16561 84.19294 assigned negative charge : -312.9831 centred at (gu) : 93.35062 88.28236 83.98408 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 170014 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16427 grid for indexing accessible points = 1.400000 m= 87032 mr = 126301 m= 32926 mr = 71558 m= 9100 mr = 26634 m= 1894 mr = 6883 m= 264 mr = 1423 m= 11 mr = 175 m= 0 mr = 7 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 5598 time to turn everything in is 1.110000 number of dielectric boundary points 68260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 15568 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) : 2.153747 object centre at (A) : -13.52700 14.76200 45.06900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3596628 0.4525989 midg,1,midg; midg,igrid,midg 0.2365932 6.7017093E-02 1,midg,midg; igrid,midg,midg 0.2913525 0.3907976 gauss-seidel spectral radius is 0.9992971 estimated iterations to convergence 298 setup time was (sec) 1.350000 now iterating at: 06:43:27 rms-change max change #iterations 10.48707 345.4078 at 10iterations 6.191478 155.7941 at 20iterations 3.648129 78.57063 at 30iterations 2.143315 37.71541 at 40iterations 1.258006 21.94141 at 50iterations 0.7386338 13.39379 at 60iterations 0.4333273 7.788396 at 70iterations 0.2540528 4.686707 at 80iterations 0.1490738 2.651611 at 90iterations 8.7233290E-02 1.633594 at 100iterations 5.1036041E-02 0.7971725 at 110iterations 2.9934159E-02 0.5498877 at 120iterations 1.7629474E-02 0.3165207 at 130iterations 1.0426849E-02 0.1832714 at 140iterations 6.2189242E-03 0.1072712 at 150iterations 3.7639602E-03 6.6772461E-02 at 160iterations 2.3340373E-03 4.5814514E-02 at 170iterations 1.4939295E-03 2.7064323E-02 at 180iterations finished qdiffx linear iterations at : 06:43:38 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 1.4939295E-03 2.7064323E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 06:43:39 12.610u 0.212s 0:13.19 97.1% 0+0k 0+0io 0pf+0w