Tue Oct 11 07:19:20 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 Tue Oct 11 2011 at 07:19:20 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5964348 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): 0.1320000 48.45000 ymin,ymax (A): -8.090000 48.85500 zmin,zma (A): 0.9669999 60.65500 x,y,z range (A): 48.31800 56.94500 59.68800 scale (grids/A): 0.5964348 object centre (A): 24.29100 20.38250 30.81100 number of atom coordinates read : 3169 total number of charged atoms : 3018 net assigned charge : -1.099989 assigned positive charge : 472.5659 centred at (gu) : 89.52026 89.36690 91.06422 assigned negative charge : -473.6670 centred at (gu) : 89.40708 89.28672 90.99131 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7357 nv = 96 ne = 84 npr = 65778 no. pairs analyzed = 65778 no. exposed pairs = 3639 no. arc points = 24638 no. surface atoms = 1249 nbur = 1920 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 4282 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3400000 number of dielectric boundary points 3370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2470 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9264 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6059108E-09 3.1822374E-09 midg,1,midg; midg,igrid,midg -4.1951003E-09 2.3805466E-09 1,midg,midg; igrid,midg,midg -5.5502940E-09 3.6161243E-09 gauss-seidel spectral radius is 0.9854934 estimated iterations to convergence 68 setup time was (sec) 0.5600000 now iterating at: 07:19:21 rms-change max change #iterations 0.1185128 18.36289 at 10iterations 1.0654468E-02 1.394330 at 20iterations 1.2835803E-03 0.1995010 at 30iterations 3.1573148E-04 5.3274155E-02 at 40iterations 9.1599992E-05 1.5705109E-02 at 50iterations finished qdiffx linear iterations at : 07:19:23 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 9.1599992E-05 1.5705109E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 07:19:24 3.389u 0.205s 0:04.12 86.8% 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 07:19:24 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.789304 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): 0.1320000 48.45000 ymin,ymax (A): -8.090000 48.85500 zmin,zma (A): 0.9669999 60.65500 x,y,z range (A): 48.31800 56.94500 59.68800 scale (grids/A): 1.789304 object centre (A): 24.29100 20.38250 30.81100 number of atom coordinates read : 3169 total number of charged atoms : 3018 net assigned charge : -1.099989 assigned positive charge : 472.5659 centred at (gu) : 88.56010 88.09982 93.19199 assigned negative charge : -473.6670 centred at (gu) : 88.22058 87.85963 92.97341 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24638 grid for indexing accessible points = 1.400000 m= 29085 mr = 58458 m= 3664 mr = 22120 m= 142 mr = 2225 m= 4 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1328 time to turn everything in is 0.5800000 number of dielectric boundary points 31257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 23543 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) : 0.5964348 object centre at (A) : 24.29100 20.38250 30.81100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9361190E-02 2.6175275E-03 midg,1,midg; midg,igrid,midg -2.4616545E-02 6.7820922E-03 1,midg,midg; igrid,midg,midg -1.5168697E-02 1.0754494E-02 gauss-seidel spectral radius is 0.9985085 estimated iterations to convergence 205 setup time was (sec) 0.8700000 now iterating at: 07:19:25 rms-change max change #iterations 4.198933 155.2410 at 10iterations 1.904890 64.65414 at 20iterations 0.8652099 31.88132 at 30iterations 0.3925861 13.05343 at 40iterations 0.1788760 5.576269 at 50iterations 8.1281967E-02 2.768867 at 60iterations 3.6993872E-02 1.179775 at 70iterations 1.6888481E-02 0.5034103 at 80iterations 7.7180597E-03 0.2399864 at 90iterations 3.5830038E-03 0.1173468 at 100iterations 1.7007436E-03 5.4317474E-02 at 110iterations 8.3127344E-04 2.9632568E-02 at 120iterations finished qdiffx linear iterations at : 07:19:32 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 8.3127344E-04 2.9632568E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 07:19:33 7.789u 0.223s 0:08.42 95.0% 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 Tue Oct 11 2011 at 07:19:33 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.683957 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): 0.1320000 48.45000 ymin,ymax (A): -8.090000 48.85500 zmin,zma (A): 0.9669999 60.65500 x,y,z range (A): 48.31800 56.94500 59.68800 scale (grids/A): 2.683957 object centre (A): 24.29100 20.38250 30.81100 number of atom coordinates read : 3169 total number of charged atoms : 3018 net assigned charge : -1.099989 assigned positive charge : 472.5659 centred at (gu) : 87.84000 87.14947 94.78764 assigned negative charge : -473.6670 centred at (gu) : 87.33069 86.78925 94.46011 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 188278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24638 grid for indexing accessible points = 1.400000 m= 96620 mr = 141610 m= 32171 mr = 80707 m= 6293 mr = 26293 m= 685 mr = 4653 m= 28 mr = 468 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 4506 time to turn everything in is 1.390000 number of dielectric boundary points 70339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 24139 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) : 1.789304 object centre at (A) : 24.29100 20.38250 30.81100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5711066 -9.4743095E-02 midg,1,midg; midg,igrid,midg -0.4096069 8.7724112E-02 1,midg,midg; igrid,midg,midg -0.1826025 0.1319164 gauss-seidel spectral radius is 0.9992286 estimated iterations to convergence 284 setup time was (sec) 1.690000 now iterating at: 07:19:35 rms-change max change #iterations 10.04249 281.0715 at 10iterations 5.782774 116.7742 at 20iterations 3.320704 66.28610 at 30iterations 1.894993 35.20087 at 40iterations 1.079234 21.61832 at 50iterations 0.6167113 10.83376 at 60iterations 0.3511502 6.189186 at 70iterations 0.1998680 3.294420 at 80iterations 0.1138159 2.258860 at 90iterations 6.4758264E-02 1.096157 at 100iterations 3.6915373E-02 0.6816025 at 110iterations 2.1028185E-02 0.3783092 at 120iterations 1.2011107E-02 0.2169228 at 130iterations 6.9059199E-03 0.1338005 at 140iterations 4.0089372E-03 7.0608139E-02 at 150iterations 2.3686080E-03 4.2455673E-02 at 160iterations 1.4365675E-03 2.9855728E-02 at 170iterations 9.0797362E-04 1.7448425E-02 at 180iterations finished qdiffx linear iterations at : 07:19:45 total time elapsed so far: 12.54000 # loops : 180 mean,max change (kT/e) : 9.0797362E-04 1.7448425E-02 energy calculations done at 12.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 07:19:46 12.713u 0.255s 0:13.25 97.8% 0+0k 0+0io 0pf+0w