Sat Oct 15 11:51:16 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 15 2011 at 11:51:16 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2354 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6556048 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): -26.73200 26.35700 ymin,ymax (A): 7.799000 50.18400 zmin,zma (A): -12.81100 41.49000 x,y,z range (A): 53.08900 42.38500 54.30100 scale (grids/A): 0.6556048 object centre (A): -0.1875000 28.99150 14.33950 number of atom coordinates read : 2354 total number of charged atoms : 2211 net assigned charge : 11.01402 assigned positive charge : 344.1993 centred at (gu) : 90.08815 90.53963 91.21809 assigned negative charge : -333.1860 centred at (gu) : 90.11120 90.49028 91.22099 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6902 nv = 96 ne = 84 npr = 47889 no. pairs analyzed = 47889 no. exposed pairs = 3048 no. arc points = 21726 no. surface atoms = 1023 nbur = 1331 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3646 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2074 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8042 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9742238E-08 3.1158628E-08 midg,1,midg; midg,igrid,midg 1.5522311E-08 3.5975372E-08 1,midg,midg; igrid,midg,midg 2.7749378E-08 2.1647537E-08 gauss-seidel spectral radius is 0.9879270 estimated iterations to convergence 74 setup time was (sec) 0.3700000 now iterating at: 11:51:16 rms-change max change #iterations 0.1485654 28.88921 at 10iterations 1.5578300E-02 2.442846 at 20iterations 1.6810452E-03 0.2314949 at 30iterations 2.2885427E-04 3.7246704E-02 at 40iterations 5.7882437E-05 1.1330605E-02 at 50iterations finished qdiffx linear iterations at : 11:51:19 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 5.7882437E-05 1.1330605E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 11:51:20 3.418u 0.193s 0:04.09 88.0% 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 15 2011 at 11:51:20 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2354 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.966815 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): -26.73200 26.35700 ymin,ymax (A): 7.799000 50.18400 zmin,zma (A): -12.81100 41.49000 x,y,z range (A): 53.08900 42.38500 54.30100 scale (grids/A): 1.966815 object centre (A): -0.1875000 28.99150 14.33950 number of atom coordinates read : 2354 total number of charged atoms : 2211 net assigned charge : 11.01402 assigned positive charge : 344.1993 centred at (gu) : 90.26400 91.61847 93.65382 assigned negative charge : -333.1860 centred at (gu) : 90.33337 91.47083 93.66300 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 27108 mr = 49901 m= 4864 mr = 19650 m= 362 mr = 2989 m= 7 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 33380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17427 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) : 0.6556048 object centre at (A) : -0.1875000 28.99150 14.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8269247E-02 2.7613074E-02 midg,1,midg; midg,igrid,midg -6.0601812E-04 2.6361406E-02 1,midg,midg; igrid,midg,midg 4.3324322E-02 5.1215924E-02 gauss-seidel spectral radius is 0.9986999 estimated iterations to convergence 220 setup time was (sec) 0.6000000 now iterating at: 11:51:21 rms-change max change #iterations 4.217137 186.8160 at 10iterations 2.007691 73.07120 at 20iterations 0.9542076 31.93075 at 30iterations 0.4571048 14.94167 at 40iterations 0.2174263 6.759843 at 50iterations 0.1033400 3.355475 at 60iterations 4.9219169E-02 1.581779 at 70iterations 2.3485295E-02 0.7436295 at 80iterations 1.1193042E-02 0.3628922 at 90iterations 5.3516030E-03 0.1723919 at 100iterations 2.5684121E-03 8.4636688E-02 at 110iterations 1.2401652E-03 4.0771484E-02 at 120iterations finished qdiffx linear iterations at : 11:51:28 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.2401652E-03 4.0771484E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 11:51:29 7.961u 0.209s 0:08.70 93.7% 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 15 2011 at 11:51:29 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2354 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.950222 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): -26.73200 26.35700 ymin,ymax (A): 7.799000 50.18400 zmin,zma (A): -12.81100 41.49000 x,y,z range (A): 53.08900 42.38500 54.30100 scale (grids/A): 2.950222 object centre (A): -0.1875000 28.99150 14.33950 number of atom coordinates read : 2354 total number of charged atoms : 2211 net assigned charge : 11.01402 assigned positive charge : 344.1993 centred at (gu) : 90.39605 92.42757 95.48071 assigned negative charge : -333.1860 centred at (gu) : 90.50007 92.20630 95.49443 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 170463 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 85922 mr = 121366 m= 32695 mr = 69316 m= 9003 mr = 26079 m= 1542 mr = 6620 m= 99 mr = 1045 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 75268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 17688 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) : 1.966815 object centre at (A) : -0.1875000 28.99150 14.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7563406 0.3045842 midg,1,midg; midg,igrid,midg -4.3512993E-02 0.2437470 1,midg,midg; igrid,midg,midg 0.3822169 0.5069116 gauss-seidel spectral radius is 0.9992789 estimated iterations to convergence 294 setup time was (sec) 1.180000 now iterating at: 11:51:30 rms-change max change #iterations 9.805815 387.3313 at 10iterations 5.777936 138.2665 at 20iterations 3.389090 73.76616 at 30iterations 1.977774 47.79778 at 40iterations 1.158699 23.96786 at 50iterations 0.6760896 12.78419 at 60iterations 0.3939282 7.832261 at 70iterations 0.2291871 5.189247 at 80iterations 0.1331968 2.526999 at 90iterations 7.7281848E-02 1.429754 at 100iterations 4.4892725E-02 0.9606950 at 110iterations 2.6063034E-02 0.4626145 at 120iterations 1.5116266E-02 0.3092041 at 130iterations 8.7692039E-03 0.1961813 at 140iterations 5.0984481E-03 9.8810196E-02 at 150iterations 2.9578942E-03 5.3732872E-02 at 160iterations 1.7293771E-03 3.2369614E-02 at 170iterations 1.0184024E-03 2.0701408E-02 at 180iterations finished qdiffx linear iterations at : 11:51:41 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 1.0184024E-03 2.0701408E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 11:51:42 12.477u 0.199s 0:13.02 97.2% 0+0k 0+0io 0pf+0w