Sat Oct 8 19:04:48 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 Sat Oct 8 2011 at 19:04:48 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 556 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: 0.6269372 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): -31.95700 17.37000 ymin,ymax (A): -23.38200 22.84000 zmin,zma (A): -12.52800 44.25600 x,y,z range (A): 49.32700 46.22200 56.78400 scale (grids/A): 0.6269372 object centre (A): -7.293500 -0.2709999 15.86400 number of atom coordinates read : 2606 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 394.6350 centred at (gu) : 88.68095 89.11230 89.84288 assigned negative charge : -390.2296 centred at (gu) : 88.57204 89.15011 89.72845 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6563 nv = 96 ne = 84 npr = 55505 no. pairs analyzed = 55505 no. exposed pairs = 2945 no. arc points = 21478 no. surface atoms = 986 nbur = 1620 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3702 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 151 time to turn everything in is 0.2000000 number of dielectric boundary points 3164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2118 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8179 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1186695E-09 1.3220826E-08 midg,1,midg; midg,igrid,midg 9.1573060E-09 1.1909874E-09 1,midg,midg; igrid,midg,midg -6.1089342E-09 9.9528545E-09 gauss-seidel spectral radius is 0.9868159 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 19:04:48 rms-change max change #iterations 0.1351265 20.29471 at 10iterations 1.2993624E-02 1.946898 at 20iterations 1.2358190E-03 0.1841888 at 30iterations 1.1380089E-04 1.7448425E-02 at 40iterations 1.0859461E-05 1.6703606E-03 at 50iterations finished qdiffx linear iterations at : 19:04:51 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.0859461E-05 1.6703606E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 19:04:52 3.578u 0.190s 0:04.04 93.0% 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 Sat Oct 8 2011 at 19:04:52 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 556 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: 1.880811 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): -31.95700 17.37000 ymin,ymax (A): -23.38200 22.84000 zmin,zma (A): -12.52800 44.25600 x,y,z range (A): 49.32700 46.22200 56.78400 scale (grids/A): 1.880811 object centre (A): -7.293500 -0.2709999 15.86400 number of atom coordinates read : 2606 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 394.6350 centred at (gu) : 86.04277 87.33642 89.52810 assigned negative charge : -390.2296 centred at (gu) : 85.71593 87.45021 89.18517 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21478 grid for indexing accessible points = 1.400000 m= 24454 mr = 50229 m= 3346 mr = 17965 m= 133 mr = 2020 m= 0 mr = 25 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 10019 time to turn everything in is 0.3600000 number of dielectric boundary points 29222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19334 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) : 0.6269372 object centre at (A) : -7.293500 -0.2709999 15.86400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6510263E-02 2.7949074E-02 midg,1,midg; midg,igrid,midg 1.7579272E-02 2.2298391E-03 1,midg,midg; igrid,midg,midg -6.9814054E-03 3.3016700E-02 gauss-seidel spectral radius is 0.9985946 estimated iterations to convergence 211 setup time was (sec) 0.6000000 now iterating at: 19:04:53 rms-change max change #iterations 4.166418 181.2079 at 10iterations 1.929988 61.71536 at 20iterations 0.8913719 32.46674 at 30iterations 0.4119435 13.83866 at 40iterations 0.1920316 6.081873 at 50iterations 8.8906623E-02 2.776077 at 60iterations 4.1175589E-02 1.236517 at 70iterations 1.9069454E-02 0.5992727 at 80iterations 8.8181058E-03 0.2757378 at 90iterations 4.1053714E-03 0.1279564 at 100iterations 1.9040937E-03 7.7009678E-02 at 110iterations 8.8209513E-04 2.9802322E-02 at 120iterations finished qdiffx linear iterations at : 19:05:00 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 8.8209513E-04 2.9802322E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 19:05:00 8.119u 0.214s 0:08.62 96.5% 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 19:05:00 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 556 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: 2.821217 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): -31.95700 17.37000 ymin,ymax (A): -23.38200 22.84000 zmin,zma (A): -12.52800 44.25600 x,y,z range (A): 49.32700 46.22200 56.78400 scale (grids/A): 2.821217 object centre (A): -7.293500 -0.2709999 15.86400 number of atom coordinates read : 2606 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 394.6350 centred at (gu) : 84.06395 86.00447 89.29206 assigned negative charge : -390.2296 centred at (gu) : 83.57389 86.17518 88.77776 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 165750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21478 grid for indexing accessible points = 1.400000 m= 81012 mr = 121483 m= 27002 mr = 66562 m= 5913 mr = 21585 m= 705 mr = 4427 m= 29 mr = 446 m= 0 mr = 3 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 33944 time to turn everything in is 0.9000000 number of dielectric boundary points 65905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 19694 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) : 1.880811 object centre at (A) : -7.293500 -0.2709999 15.86400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4761420E-02 0.3195258 midg,1,midg; midg,igrid,midg 0.2303240 1.6413828E-02 1,midg,midg; igrid,midg,midg -5.9370678E-02 0.4029367 gauss-seidel spectral radius is 0.9992414 estimated iterations to convergence 287 setup time was (sec) 1.140000 now iterating at: 19:05:02 rms-change max change #iterations 9.629546 302.6974 at 10iterations 5.523159 123.1956 at 20iterations 3.145469 58.71221 at 30iterations 1.795809 33.17157 at 40iterations 1.021148 17.75619 at 50iterations 0.5814007 10.45108 at 60iterations 0.3315049 5.821849 at 70iterations 0.1890827 3.358239 at 80iterations 0.1075393 2.054499 at 90iterations 6.1294064E-02 1.150570 at 100iterations 3.4890261E-02 0.6359091 at 110iterations 1.9861255E-02 0.3581657 at 120iterations 1.1316539E-02 0.2386227 at 130iterations 6.4317896E-03 0.1154709 at 140iterations 3.6669467E-03 6.9576263E-02 at 150iterations 2.0913761E-03 3.9688110E-02 at 160iterations 1.1898258E-03 2.1697998E-02 at 170iterations 6.7905092E-04 1.1964798E-02 at 180iterations finished qdiffx linear iterations at : 19:05:14 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 6.7905092E-04 1.1964798E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 19:05:14 12.952u 0.237s 0:13.48 97.7% 0+0k 0+0io 0pf+0w