Sat Oct 8 15:46:56 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 Sat Oct 8 2011 at 15:46:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2415 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6499078 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): -18.83100 29.57500 ymin,ymax (A): 36.97500 82.52600 zmin,zma (A): -18.97400 35.80300 x,y,z range (A): 48.40600 45.55100 54.77700 scale (grids/A): 0.6499078 object centre (A): 5.372000 59.75050 8.414499 number of atom coordinates read : 2415 total number of charged atoms : 2349 net assigned charge : 5.000004 assigned positive charge : 359.9079 centred at (gu) : 89.12074 91.06630 90.52441 assigned negative charge : -354.9086 centred at (gu) : 89.06961 90.96786 90.54408 start vw surface at 0.1300000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6894 nv = 96 ne = 84 npr = 48321 no. pairs analyzed = 48321 no. exposed pairs = 2996 no. arc points = 20812 no. surface atoms = 1021 nbur = 1394 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 3823 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3500000 number of dielectric boundary points 3413 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2038 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8289 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1019270E-08 7.5578317E-09 midg,1,midg; midg,igrid,midg -3.3044638E-09 2.8920747E-08 1,midg,midg; igrid,midg,midg 2.7865450E-09 1.3841255E-08 gauss-seidel spectral radius is 0.9877166 estimated iterations to convergence 74 setup time was (sec) 0.6900000 now iterating at: 15:46:58 rms-change max change #iterations 0.1477029 21.30125 at 10iterations 1.5171138E-02 2.156969 at 20iterations 1.5640347E-03 0.2178936 at 30iterations 1.7621176E-04 2.5657654E-02 at 40iterations 2.3949917E-05 3.8261414E-03 at 50iterations finished qdiffx linear iterations at : 15:47:01 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 2.3949917E-05 3.8261414E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 15:47:02 4.545u 0.433s 0:05.28 94.1% 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 Sat Oct 8 2011 at 15:47:02 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 = 2415 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.949724 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): -18.83100 29.57500 ymin,ymax (A): 36.97500 82.52600 zmin,zma (A): -18.97400 35.80300 x,y,z range (A): 48.40600 45.55100 54.77700 scale (grids/A): 1.949724 object centre (A): 5.372000 59.75050 8.414499 number of atom coordinates read : 2415 total number of charged atoms : 2349 net assigned charge : 5.000004 assigned positive charge : 359.9079 centred at (gu) : 87.36144 93.19813 91.57293 assigned negative charge : -354.9086 centred at (gu) : 87.20879 92.90329 91.63210 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 74415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20812 grid for indexing accessible points = 1.400000 m= 27859 mr = 52056 m= 5046 mr = 20674 m= 345 mr = 3439 m= 2 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 908 time to turn everything in is 0.7700000 number of dielectric boundary points 31345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 18505 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) : 0.6499078 object centre at (A) : 5.372000 59.75050 8.414499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5862508E-02 3.0944457E-03 midg,1,midg; midg,igrid,midg -2.9121065E-03 2.5447039E-02 1,midg,midg; igrid,midg,midg -3.2047272E-02 1.1549259E-02 gauss-seidel spectral radius is 0.9986776 estimated iterations to convergence 218 setup time was (sec) 1.110000 now iterating at: 15:47:03 rms-change max change #iterations 4.242763 224.9230 at 10iterations 2.011608 78.73419 at 20iterations 0.9509116 33.42746 at 30iterations 0.4528433 14.99954 at 40iterations 0.2147776 6.253249 at 50iterations 0.1021482 3.027161 at 60iterations 4.8430968E-02 1.841036 at 70iterations 2.2962946E-02 0.7018604 at 80iterations 1.0916535E-02 0.3577366 at 90iterations 5.1765963E-03 0.1562119 at 100iterations 2.4650034E-03 7.4430466E-02 at 110iterations 1.1738215E-03 3.5202026E-02 at 120iterations finished qdiffx linear iterations at : 15:47:12 total time elapsed so far: 10.21000 # loops : 120 mean,max change (kT/e) : 1.1738215E-03 3.5202026E-02 energy calculations done at 10.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.42000 DelPhi exited at 15:47:13 10.422u 0.430s 0:11.13 97.4% 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 Sat Oct 8 2011 at 15:47:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2415 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.924585 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): -18.83100 29.57500 ymin,ymax (A): 36.97500 82.52600 zmin,zma (A): -18.97400 35.80300 x,y,z range (A): 48.40600 45.55100 54.77700 scale (grids/A): 2.924585 object centre (A): 5.372000 59.75050 8.414499 number of atom coordinates read : 2415 total number of charged atoms : 2349 net assigned charge : 5.000004 assigned positive charge : 359.9079 centred at (gu) : 86.04202 94.79708 92.35923 assigned negative charge : -354.9086 centred at (gu) : 85.81317 94.35500 92.44810 start vw surface at 0.1400000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 172156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20812 grid for indexing accessible points = 1.400000 m= 88535 mr = 126095 m= 34035 mr = 72571 m= 9418 mr = 27741 m= 1551 mr = 7392 m= 106 mr = 1144 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 2941 time to turn everything in is 2.020000 number of dielectric boundary points 70798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 18791 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) : 1.949724 object centre at (A) : 5.372000 59.75050 8.414499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2178066 -7.0425950E-02 midg,1,midg; midg,igrid,midg -6.5955184E-02 0.1877984 1,midg,midg; igrid,midg,midg -0.3611108 0.1044881 gauss-seidel spectral radius is 0.9992684 estimated iterations to convergence 292 setup time was (sec) 2.380000 now iterating at: 15:47:16 rms-change max change #iterations 9.855789 534.7933 at 10iterations 5.780005 140.3917 at 20iterations 3.367860 68.05019 at 30iterations 1.965437 41.41190 at 40iterations 1.142305 19.71946 at 50iterations 0.6646814 12.64110 at 60iterations 0.3846473 7.461304 at 70iterations 0.2228126 4.650948 at 80iterations 0.1286462 2.356830 at 90iterations 7.4318424E-02 1.381628 at 100iterations 4.3005690E-02 0.8006821 at 110iterations 2.4865614E-02 0.4796028 at 120iterations 1.4313415E-02 0.2616272 at 130iterations 8.2742497E-03 0.1586723 at 140iterations 4.7798050E-03 8.3759308E-02 at 150iterations 2.7480093E-03 4.7424316E-02 at 160iterations 1.5889910E-03 2.9088974E-02 at 170iterations 9.1664039E-04 1.5846252E-02 at 180iterations finished qdiffx linear iterations at : 15:47:31 total time elapsed so far: 17.58000 # loops : 180 mean,max change (kT/e) : 9.1664039E-04 1.5846252E-02 energy calculations done at 17.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.80000 DelPhi exited at 15:47:31 17.807u 0.475s 0:18.56 98.4% 0+0k 0+0io 0pf+0w