Wed Dec 21 14:20:44 PST 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 Wed Dec 21 2011 at 14:20:44 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 = 1937 !!! WARNING: MET 145 has a net charge of -0.0720 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: 0.6381301 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): -35.08800 11.00700 ymin,ymax (A): 1.270000 40.78600 zmin,zma (A): -0.4540000 55.33400 x,y,z range (A): 46.09500 39.51600 55.78800 scale (grids/A): 0.6381301 object centre (A): -12.04050 21.02800 27.44000 number of atom coordinates read : 1937 total number of charged atoms : 1805 net assigned charge : -7.1993321E-02 assigned positive charge : 282.2031 centred at (gu) : 90.25323 89.57131 90.12833 assigned negative charge : -282.2753 centred at (gu) : 90.15114 89.70834 90.10209 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5415 nv = 96 ne = 84 npr = 40238 no. pairs analyzed = 40238 no. exposed pairs = 2325 no. arc points = 16550 no. surface atoms = 794 nbur = 1143 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 281 mr = 3093 m= 0 mr = 45 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.1600000 number of dielectric boundary points 2558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1655 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6343 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2258115E-09 2.0007498E-09 midg,1,midg; midg,igrid,midg 1.1780840E-08 -1.0368641E-08 1,midg,midg; igrid,midg,midg -8.0370510E-09 8.4340614E-09 gauss-seidel spectral radius is 0.9872185 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 14:20:45 rms-change max change #iterations 0.1202013 20.34179 at 10iterations 1.1775711E-02 1.836395 at 20iterations 1.1592187E-03 0.1781654 at 30iterations 1.1346607E-04 1.9402504E-02 at 40iterations 1.0947640E-05 1.7137527E-03 at 50iterations finished qdiffx linear iterations at : 14:20:48 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 1.0947640E-05 1.7137527E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 14:20:49 4.025u 0.249s 0:04.95 86.0% 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 Wed Dec 21 2011 at 14:20:49 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 = 1937 !!! WARNING: MET 145 has a net charge of -0.0720 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: 1.914390 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): -35.08800 11.00700 ymin,ymax (A): 1.270000 40.78600 zmin,zma (A): -0.4540000 55.33400 x,y,z range (A): 46.09500 39.51600 55.78800 scale (grids/A): 1.914390 object centre (A): -12.04050 21.02800 27.44000 number of atom coordinates read : 1937 total number of charged atoms : 1805 net assigned charge : -7.1993321E-02 assigned positive charge : 282.2031 centred at (gu) : 90.75976 88.71394 90.38512 assigned negative charge : -282.2753 centred at (gu) : 90.45352 89.12518 90.30643 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 57876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16550 grid for indexing accessible points = 1.400000 m= 22013 mr = 40330 m= 3529 mr = 17017 m= 185 mr = 2396 m= 4 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 899 time to turn everything in is 0.3400000 number of dielectric boundary points 23791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 14205 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) : 0.6381301 object centre at (A) : -12.04050 21.02800 27.44000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0481208E-03 1.3769300E-02 midg,1,midg; midg,igrid,midg 3.6746606E-03 -1.8967081E-02 1,midg,midg; igrid,midg,midg -6.3904668E-03 -2.8022313E-03 gauss-seidel spectral radius is 0.9985709 estimated iterations to convergence 210 setup time was (sec) 0.7400000 now iterating at: 14:20:50 rms-change max change #iterations 3.561483 164.6490 at 10iterations 1.637969 60.94043 at 20iterations 0.7584689 26.16320 at 30iterations 0.3495825 13.61905 at 40iterations 0.1600684 5.583199 at 50iterations 7.3653437E-02 2.731236 at 60iterations 3.3983499E-02 1.392273 at 70iterations 1.5626349E-02 0.6086426 at 80iterations 7.1876235E-03 0.2629657 at 90iterations 3.3133805E-03 0.1204224 at 100iterations 1.5239991E-03 5.1821232E-02 at 110iterations 6.9987873E-04 2.4677277E-02 at 120iterations finished qdiffx linear iterations at : 14:20:59 total time elapsed so far: 9.910000 # loops : 120 mean,max change (kT/e) : 6.9987873E-04 2.4677277E-02 energy calculations done at 9.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.06000 DelPhi exited at 14:21:00 10.060u 0.449s 0:11.00 95.4% 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 Wed Dec 21 2011 at 14:21:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1937 !!! WARNING: MET 145 has a net charge of -0.0720 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: 2.871585 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): -35.08800 11.00700 ymin,ymax (A): 1.270000 40.78600 zmin,zma (A): -0.4540000 55.33400 x,y,z range (A): 46.09500 39.51600 55.78800 scale (grids/A): 2.871585 object centre (A): -12.04050 21.02800 27.44000 number of atom coordinates read : 1937 total number of charged atoms : 1805 net assigned charge : -7.1993321E-02 assigned positive charge : 282.2031 centred at (gu) : 91.13952 88.07087 90.57766 assigned negative charge : -282.2753 centred at (gu) : 90.68034 88.68787 90.45973 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 133384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16550 grid for indexing accessible points = 1.400000 m= 70045 mr = 96989 m= 26697 mr = 58761 m= 6422 mr = 22398 m= 841 mr = 5044 m= 41 mr = 607 m= 0 mr = 20 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 3014 time to turn everything in is 0.9400000 number of dielectric boundary points 53611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 14440 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) : 1.914390 object centre at (A) : -12.04050 21.02800 27.44000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8059310E-02 6.7844622E-02 midg,1,midg; midg,igrid,midg 1.2725051E-02 -0.2140253 1,midg,midg; igrid,midg,midg -8.8075005E-02 -9.1717623E-02 gauss-seidel spectral radius is 0.9992241 estimated iterations to convergence 283 setup time was (sec) 1.370000 now iterating at: 14:21:03 rms-change max change #iterations 8.338073 309.0132 at 10iterations 4.765613 155.5201 at 20iterations 2.706880 62.47278 at 30iterations 1.538684 32.61980 at 40iterations 0.8713492 16.86170 at 50iterations 0.4949064 10.12525 at 60iterations 0.2794845 5.669244 at 70iterations 0.1582571 2.987528 at 80iterations 8.9536615E-02 1.970503 at 90iterations 5.0591614E-02 1.100609 at 100iterations 2.8607363E-02 0.5699148 at 110iterations 1.6193660E-02 0.3381195 at 120iterations 9.1958726E-03 0.1801977 at 130iterations 5.1768674E-03 0.1211503 at 140iterations 2.9354563E-03 5.9407711E-02 at 150iterations 1.6633235E-03 3.1390846E-02 at 160iterations 9.3704392E-04 1.8976212E-02 at 170iterations 5.3158327E-04 1.0255098E-02 at 180iterations finished qdiffx linear iterations at : 14:21:17 total time elapsed so far: 16.24000 # loops : 180 mean,max change (kT/e) : 5.3158327E-04 1.0255098E-02 energy calculations done at 16.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.38000 DelPhi exited at 14:21:22 16.386u 0.458s 0:21.89 76.8% 0+0k 0+0io 0pf+0w