Tue Oct 11 07:47:47 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 07:47:47 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2679 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: 0.6360550 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): -13.32300 42.64700 ymin,ymax (A): -22.41500 25.32200 zmin,zma (A): -5.482000 40.33000 x,y,z range (A): 55.97000 47.73700 45.81200 scale (grids/A): 0.6360550 object centre (A): 14.66200 1.453501 17.42400 number of atom coordinates read : 2679 total number of charged atoms : 2322 net assigned charge : 6.500006 assigned positive charge : 370.0011 centred at (gu) : 89.59598 88.84829 89.29582 assigned negative charge : -363.5017 centred at (gu) : 89.68298 88.81643 89.43954 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6581 nv = 96 ne = 84 npr = 50305 no. pairs analyzed = 50305 no. exposed pairs = 2889 no. arc points = 19819 no. surface atoms = 997 nbur = 1682 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3758 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2026 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7954 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5829056E-08 -5.0502300E-09 midg,1,midg; midg,igrid,midg 6.5634951E-09 8.9913099E-09 1,midg,midg; igrid,midg,midg 1.8287398E-08 -2.0696100E-10 gauss-seidel spectral radius is 0.9871753 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 07:47:48 rms-change max change #iterations 0.1373467 21.61511 at 10iterations 1.3775310E-02 2.130571 at 20iterations 1.4531137E-03 0.2350445 at 30iterations 1.8183314E-04 2.4256706E-02 at 40iterations 2.8579763E-05 4.2419434E-03 at 50iterations finished qdiffx linear iterations at : 07:47:51 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 2.8579763E-05 4.2419434E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 07:47:52 4.068u 0.258s 0:04.94 87.2% 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 07:47:52 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2679 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: 1.908165 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): -13.32300 42.64700 ymin,ymax (A): -22.41500 25.32200 zmin,zma (A): -5.482000 40.33000 x,y,z range (A): 55.97000 47.73700 45.81200 scale (grids/A): 1.908165 object centre (A): 14.66200 1.453501 17.42400 number of atom coordinates read : 2679 total number of charged atoms : 2322 net assigned charge : 6.500006 assigned positive charge : 370.0011 centred at (gu) : 88.78713 86.54462 87.88675 assigned negative charge : -363.5017 centred at (gu) : 89.04886 86.44915 88.31834 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19819 grid for indexing accessible points = 1.400000 m= 26048 mr = 50456 m= 3856 mr = 19718 m= 188 mr = 2367 m= 5 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 28467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 18248 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) : 0.6360550 object centre at (A) : 14.66200 1.453501 17.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9777327E-02 -3.3393952E-03 midg,1,midg; midg,igrid,midg 5.9249280E-03 1.9927379E-02 1,midg,midg; igrid,midg,midg 2.0769795E-02 7.9821767E-03 gauss-seidel spectral radius is 0.9986181 estimated iterations to convergence 213 setup time was (sec) 0.9400000 now iterating at: 07:47:54 rms-change max change #iterations 4.070883 164.9356 at 10iterations 1.907351 67.85026 at 20iterations 0.8875071 30.17045 at 30iterations 0.4156812 13.97614 at 40iterations 0.1949639 6.962654 at 50iterations 9.1183133E-02 2.866230 at 60iterations 4.2614322E-02 1.402627 at 70iterations 1.9909112E-02 0.6390114 at 80iterations 9.3184300E-03 0.2911224 at 90iterations 4.3672891E-03 0.1344709 at 100iterations 2.0661287E-03 6.6360474E-02 at 110iterations 9.8291622E-04 3.1290054E-02 at 120iterations finished qdiffx linear iterations at : 07:48:02 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 9.8291622E-04 3.1290054E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 07:48:02 9.324u 0.303s 0:10.15 94.7% 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 Tue Oct 11 2011 at 07:48:03 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2679 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: 2.862247 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): -13.32300 42.64700 ymin,ymax (A): -22.41500 25.32200 zmin,zma (A): -5.482000 40.33000 x,y,z range (A): 55.97000 47.73700 45.81200 scale (grids/A): 2.862247 object centre (A): 14.66200 1.453501 17.42400 number of atom coordinates read : 2679 total number of charged atoms : 2322 net assigned charge : 6.500006 assigned positive charge : 370.0011 centred at (gu) : 88.18060 84.81677 86.83005 assigned negative charge : -363.5017 centred at (gu) : 88.57320 84.67369 87.47746 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 163884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19819 grid for indexing accessible points = 1.400000 m= 84792 mr = 121603 m= 30192 mr = 70649 m= 6674 mr = 24532 m= 890 mr = 4969 m= 51 mr = 615 m= 0 mr = 24 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.640000 number of dielectric boundary points 64091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 18569 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) : 1.908165 object centre at (A) : 14.66200 1.453501 17.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3794426 -9.4438709E-02 midg,1,midg; midg,igrid,midg 6.5503120E-02 0.2202891 1,midg,midg; igrid,midg,midg 8.3905034E-02 2.8007612E-02 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 1.960000 now iterating at: 07:48:05 rms-change max change #iterations 9.500989 334.2976 at 10iterations 5.486905 116.8543 at 20iterations 3.164489 66.97224 at 30iterations 1.820096 35.53325 at 40iterations 1.043246 21.40791 at 50iterations 0.5982752 10.85413 at 60iterations 0.3433202 6.599960 at 70iterations 0.1965786 3.620430 at 80iterations 0.1122668 2.084881 at 90iterations 6.4273447E-02 1.297953 at 100iterations 3.6708202E-02 0.6799908 at 110iterations 2.0966234E-02 0.4218445 at 120iterations 1.2013438E-02 0.2320366 at 130iterations 6.8710088E-03 0.1173396 at 140iterations 3.9554131E-03 7.1426392E-02 at 150iterations 2.2798360E-03 4.1841507E-02 at 160iterations 1.3253152E-03 2.2914886E-02 at 170iterations 7.8051857E-04 1.4434814E-02 at 180iterations finished qdiffx linear iterations at : 07:48:18 total time elapsed so far: 15.36000 # loops : 180 mean,max change (kT/e) : 7.8051857E-04 1.4434814E-02 energy calculations done at 15.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.54000 DelPhi exited at 07:48:19 15.543u 0.301s 0:16.31 97.1% 0+0k 0+0io 0pf+0w