Sat Oct 8 20:31:14 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 20:31:14 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 593 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6196045 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): -31.30700 17.65600 ymin,ymax (A): -23.56600 22.41500 zmin,zma (A): -12.42900 45.02700 x,y,z range (A): 48.96300 45.98100 57.45600 scale (grids/A): 0.6196045 object centre (A): -6.825500 -0.5755005 16.29900 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.51392 89.30661 89.59258 assigned negative charge : -388.8955 centred at (gu) : 88.38999 89.36578 89.47237 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6436 nv = 96 ne = 84 npr = 54952 no. pairs analyzed = 54952 no. exposed pairs = 3035 no. arc points = 21734 no. surface atoms = 1022 nbur = 1584 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 312 mr = 3557 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.2000000 number of dielectric boundary points 3158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2158 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8042 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7042308E-09 1.0517945E-08 midg,1,midg; midg,igrid,midg 8.8299581E-09 -1.3486504E-10 1,midg,midg; igrid,midg,midg -6.4310934E-09 8.4816003E-09 gauss-seidel spectral radius is 0.9865056 estimated iterations to convergence 70 setup time was (sec) 0.4100000 now iterating at: 20:31:14 rms-change max change #iterations 0.1262443 17.17531 at 10iterations 1.1503490E-02 1.895350 at 20iterations 1.0936494E-03 0.1539612 at 30iterations 1.0900093E-04 1.6905785E-02 at 40iterations 1.1582884E-05 1.9493103E-03 at 50iterations finished qdiffx linear iterations at : 20:31:17 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.1582884E-05 1.9493103E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 20:31:18 3.542u 0.191s 0:04.02 92.7% 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 20:31:18 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 593 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.858814 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): -31.30700 17.65600 ymin,ymax (A): -23.56600 22.41500 zmin,zma (A): -12.42900 45.02700 x,y,z range (A): 48.96300 45.98100 57.45600 scale (grids/A): 1.858814 object centre (A): -6.825500 -0.5755005 16.29900 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.54125 87.91920 88.77715 assigned negative charge : -388.8955 centred at (gu) : 85.16969 88.09684 88.41687 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21734 grid for indexing accessible points = 1.400000 m= 23862 mr = 48900 m= 3171 mr = 17394 m= 157 mr = 1946 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4907 time to turn everything in is 0.3500000 number of dielectric boundary points 29050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19357 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) : 0.6196045 object centre at (A) : -6.825500 -0.5755005 16.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6593777E-02 3.0180758E-02 midg,1,midg; midg,igrid,midg 1.4178172E-02 -6.8576884E-04 1,midg,midg; igrid,midg,midg -5.3776358E-03 3.7535544E-02 gauss-seidel spectral radius is 0.9985646 estimated iterations to convergence 209 setup time was (sec) 0.5800000 now iterating at: 20:31:19 rms-change max change #iterations 4.022368 168.7852 at 10iterations 1.850367 69.63429 at 20iterations 0.8494429 29.86936 at 30iterations 0.3887429 13.54768 at 40iterations 0.1793976 5.942963 at 50iterations 8.2277395E-02 2.872826 at 60iterations 3.7987664E-02 1.493399 at 70iterations 1.7393585E-02 0.5205841 at 80iterations 7.9936888E-03 0.2992206 at 90iterations 3.6797998E-03 0.1205196 at 100iterations 1.6934465E-03 5.7565689E-02 at 110iterations 7.8338420E-04 2.4768353E-02 at 120iterations finished qdiffx linear iterations at : 20:31:26 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 7.8338420E-04 2.4768353E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 20:31:26 8.016u 0.219s 0:08.50 96.7% 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 20:31:27 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 593 has a net charge of 1.4000 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: 2.788220 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): -31.30700 17.65600 ymin,ymax (A): -23.56600 22.41500 zmin,zma (A): -12.42900 45.02700 x,y,z range (A): 48.96300 45.98100 57.45600 scale (grids/A): 2.788220 object centre (A): -6.825500 -0.5755005 16.29900 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.31172 86.87875 88.16560 assigned negative charge : -388.8955 centred at (gu) : 82.75452 87.14527 87.62530 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 162614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21734 grid for indexing accessible points = 1.400000 m= 79156 mr = 118386 m= 26031 mr = 64925 m= 5792 mr = 20747 m= 691 mr = 4315 m= 33 mr = 426 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 16999 time to turn everything in is 0.9200000 number of dielectric boundary points 65504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19725 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) : 1.858814 object centre at (A) : -6.825500 -0.5755005 16.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1021994 0.4067750 midg,1,midg; midg,igrid,midg 0.1705340 -4.5813676E-02 1,midg,midg; igrid,midg,midg -6.1218556E-02 0.5061054 gauss-seidel spectral radius is 0.9992340 estimated iterations to convergence 285 setup time was (sec) 1.180000 now iterating at: 20:31:28 rms-change max change #iterations 9.456942 282.4447 at 10iterations 5.445230 139.1892 at 20iterations 3.109409 61.20679 at 30iterations 1.774706 37.67678 at 40iterations 1.011835 20.60377 at 50iterations 0.5766343 14.21785 at 60iterations 0.3282347 6.661070 at 70iterations 0.1868163 3.419277 at 80iterations 0.1062691 2.210699 at 90iterations 6.0544387E-02 1.247162 at 100iterations 3.4434516E-02 0.6588912 at 110iterations 1.9588154E-02 0.3906212 at 120iterations 1.1130590E-02 0.2018776 at 130iterations 6.3509224E-03 0.1136532 at 140iterations 3.6177742E-03 8.6175919E-02 at 150iterations 2.0656281E-03 4.3773651E-02 at 160iterations 1.1818068E-03 2.3157120E-02 at 170iterations 6.7768205E-04 1.2669563E-02 at 180iterations finished qdiffx linear iterations at : 20:31:46 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 6.7768205E-04 1.2669563E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 20:31:46 13.469u 1.098s 0:19.82 73.4% 0+0k 0+0io 0pf+0w