Tue Oct 11 06:32:43 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 Tue Oct 11 2011 at 06:32:43 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7076972 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): -40.53500 -0.3960000 ymin,ymax (A): -27.47400 18.78400 zmin,zma (A): -15.07000 35.23400 x,y,z range (A): 40.13900 46.25800 50.30400 scale (grids/A): 0.7076972 object centre (A): -20.46550 -4.344999 10.08200 number of atom coordinates read : 2064 total number of charged atoms : 1951 net assigned charge : 5.851010 assigned positive charge : 319.2160 centred at (gu) : 91.18174 89.95887 88.72856 assigned negative charge : -313.3651 centred at (gu) : 91.22431 90.09105 88.67115 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6966 nv = 96 ne = 84 npr = 41037 no. pairs analyzed = 41037 no. exposed pairs = 2459 no. arc points = 16976 no. surface atoms = 840 nbur = 1224 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 4006 m= 4 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2500000 number of dielectric boundary points 3335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1628 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7787 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6787212E-08 6.1736429E-08 midg,1,midg; midg,igrid,midg 1.1613320E-07 -1.6288951E-08 1,midg,midg; igrid,midg,midg 5.7004272E-08 3.5840380E-08 gauss-seidel spectral radius is 0.9895896 estimated iterations to convergence 80 setup time was (sec) 0.4900000 now iterating at: 06:32:44 rms-change max change #iterations 0.2107946 29.94942 at 10iterations 2.6208777E-02 3.439980 at 20iterations 3.5186566E-03 0.4841919 at 30iterations 5.4966082E-04 7.2463989E-02 at 40iterations 1.1225656E-04 1.4404297E-02 at 50iterations finished qdiffx linear iterations at : 06:32:46 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 1.1225656E-04 1.4404297E-02 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 06:32:47 3.252u 0.177s 0:03.73 91.6% 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 06:32:47 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.123091 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): -40.53500 -0.3960000 ymin,ymax (A): -27.47400 18.78400 zmin,zma (A): -15.07000 35.23400 x,y,z range (A): 40.13900 46.25800 50.30400 scale (grids/A): 2.123091 object centre (A): -20.46550 -4.344999 10.08200 number of atom coordinates read : 2064 total number of charged atoms : 1951 net assigned charge : 5.851010 assigned positive charge : 319.2160 centred at (gu) : 93.54514 89.87644 86.18569 assigned negative charge : -313.3651 centred at (gu) : 93.67313 90.27316 86.01348 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 29969 mr = 52700 m= 6064 mr = 22914 m= 629 mr = 4213 m= 18 mr = 356 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 553 time to turn everything in is 0.5500000 number of dielectric boundary points 30706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15479 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) : 0.7076972 object centre at (A) : -20.46550 -4.344999 10.08200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0357295E-02 3.1223893E-02 midg,1,midg; midg,igrid,midg 4.5021191E-02 7.2166482E-03 1,midg,midg; igrid,midg,midg 1.6911564E-02 2.3656907E-02 gauss-seidel spectral radius is 0.9988286 estimated iterations to convergence 231 setup time was (sec) 0.8500000 now iterating at: 06:32:48 rms-change max change #iterations 4.675376 248.6805 at 10iterations 2.317378 97.03810 at 20iterations 1.154645 34.18133 at 30iterations 0.5711732 17.23880 at 40iterations 0.2840940 8.567209 at 50iterations 0.1411599 4.220904 at 60iterations 7.0251457E-02 2.143730 at 70iterations 3.4958430E-02 1.055219 at 80iterations 1.7411087E-02 0.5463018 at 90iterations 8.7345270E-03 0.2701225 at 100iterations 4.3752748E-03 0.1340618 at 110iterations 2.2338131E-03 6.2049866E-02 at 120iterations finished qdiffx linear iterations at : 06:32:54 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 2.2338131E-03 6.2049866E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 06:32:55 7.484u 0.231s 0:08.35 92.3% 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 06:32:55 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.184637 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): -40.53500 -0.3960000 ymin,ymax (A): -27.47400 18.78400 zmin,zma (A): -15.07000 35.23400 x,y,z range (A): 40.13900 46.25800 50.30400 scale (grids/A): 3.184637 object centre (A): -20.46550 -4.344999 10.08200 number of atom coordinates read : 2064 total number of charged atoms : 1951 net assigned charge : 5.851010 assigned positive charge : 319.2160 centred at (gu) : 95.31768 89.81481 84.27852 assigned negative charge : -313.3651 centred at (gu) : 95.50964 90.40969 84.02020 start vw surface at 0.1500000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 170930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 92927 mr = 126684 m= 38428 mr = 77609 m= 11562 mr = 31922 m= 2616 mr = 9188 m= 363 mr = 2011 m= 21 mr = 276 m= 0 mr = 3 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 1913 time to turn everything in is 1.790000 number of dielectric boundary points 69154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 15608 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) : 2.123091 object centre at (A) : -20.46550 -4.344999 10.08200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3363082 0.1437076 midg,1,midg; midg,igrid,midg 0.3575866 4.3269530E-02 1,midg,midg; igrid,midg,midg 0.1281650 0.2413208 gauss-seidel spectral radius is 0.9992969 estimated iterations to convergence 298 setup time was (sec) 2.110000 now iterating at: 06:32:58 rms-change max change #iterations 10.35824 307.6752 at 10iterations 6.116484 201.2811 at 20iterations 3.609931 89.29608 at 30iterations 2.130739 40.36759 at 40iterations 1.250534 25.41101 at 50iterations 0.7363579 13.02732 at 60iterations 0.4315012 8.029682 at 70iterations 0.2529803 4.735405 at 80iterations 0.1482402 2.449878 at 90iterations 8.7030448E-02 1.543594 at 100iterations 5.1173925E-02 0.9425631 at 110iterations 3.0223582E-02 0.5387726 at 120iterations 1.7979708E-02 0.3399200 at 130iterations 1.0863543E-02 0.1993752 at 140iterations 6.7224819E-03 0.1349792 at 150iterations 4.3038093E-03 8.3114624E-02 at 160iterations 2.8956647E-03 5.5419922E-02 at 170iterations 2.0513386E-03 4.0637970E-02 at 180iterations finished qdiffx linear iterations at : 06:33:09 total time elapsed so far: 13.51000 # loops : 180 mean,max change (kT/e) : 2.0513386E-03 4.0637970E-02 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 06:33:10 13.697u 0.200s 0:14.25 97.4% 0+0k 0+0io 0pf+0w