Sat Oct 15 13:00:57 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 13:00:57 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 !!! WARNING: HIR 137 has a net charge of 0.5140 !!! WARNING: SEP 288 has a net charge of -0.4750 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: 0.6125996 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): -13.89900 44.21400 ymin,ymax (A): -24.67200 25.45500 zmin,zma (A): 21.54600 68.30400 x,y,z range (A): 58.11300 50.12700 46.75800 scale (grids/A): 0.6125996 object centre (A): 15.15750 0.3915005 44.92500 number of atom coordinates read : 2785 total number of charged atoms : 2643 net assigned charge : 3.539007 assigned positive charge : 423.6803 centred at (gu) : 89.36926 89.14840 89.90749 assigned negative charge : -420.1424 centred at (gu) : 89.31454 89.26430 89.76215 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6863 nv = 96 ne = 84 npr = 56133 no. pairs analyzed = 56133 no. exposed pairs = 3610 no. arc points = 24865 no. surface atoms = 1209 nbur = 1576 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3566 m= 0 mr = 30 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3100000 number of dielectric boundary points 3595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2538 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8536 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4449384E-09 1.0301364E-08 midg,1,midg; midg,igrid,midg 1.0736052E-08 -3.7368886E-09 1,midg,midg; igrid,midg,midg -1.1085032E-09 4.6885056E-09 gauss-seidel spectral radius is 0.9862202 estimated iterations to convergence 70 setup time was (sec) 0.5500000 now iterating at: 13:00:58 rms-change max change #iterations 0.1229962 21.39485 at 10iterations 1.1090348E-02 1.698305 at 20iterations 1.0286567E-03 0.1436768 at 30iterations 1.1786266E-04 1.8699646E-02 at 40iterations 2.5275051E-05 5.0847530E-03 at 50iterations finished qdiffx linear iterations at : 13:01:00 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.5275051E-05 5.0847530E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 13:01:01 3.432u 0.168s 0:03.89 92.2% 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 Sat Oct 15 2011 at 13:01:01 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 !!! WARNING: HIR 137 has a net charge of 0.5140 !!! WARNING: SEP 288 has a net charge of -0.4750 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: 1.837799 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): -13.89900 44.21400 ymin,ymax (A): -24.67200 25.45500 zmin,zma (A): 21.54600 68.30400 x,y,z range (A): 58.11300 50.12700 46.75800 scale (grids/A): 1.837799 object centre (A): 15.15750 0.3915005 44.92500 number of atom coordinates read : 2785 total number of charged atoms : 2643 net assigned charge : 3.539007 assigned positive charge : 423.6803 centred at (gu) : 88.10706 87.44445 89.72169 assigned negative charge : -420.1424 centred at (gu) : 87.94343 87.79272 89.28618 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24865 grid for indexing accessible points = 1.400000 m= 25179 mr = 50786 m= 3501 mr = 17616 m= 210 mr = 1936 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 33150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 20683 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) : 0.6125996 object centre at (A) : 15.15750 0.3915005 44.92500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0047902E-03 1.5872577E-02 midg,1,midg; midg,igrid,midg 2.5100660E-02 5.7454770E-03 1,midg,midg; igrid,midg,midg -4.3414157E-02 -4.1131815E-03 gauss-seidel spectral radius is 0.9985621 estimated iterations to convergence 209 setup time was (sec) 0.8500000 now iterating at: 13:01:02 rms-change max change #iterations 4.179674 179.5478 at 10iterations 1.915899 75.00480 at 20iterations 0.8776551 34.65002 at 30iterations 0.4033236 13.35421 at 40iterations 0.1841635 5.980093 at 50iterations 8.4730506E-02 2.791962 at 60iterations 3.8749333E-02 1.285946 at 70iterations 1.7833043E-02 0.6183281 at 80iterations 8.1561320E-03 0.2739077 at 90iterations 3.7488597E-03 0.1303673 at 100iterations 1.7217138E-03 5.2585602E-02 at 110iterations 7.9454744E-04 2.6198387E-02 at 120iterations finished qdiffx linear iterations at : 13:01:08 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 7.9454744E-04 2.6198387E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 13:01:09 7.690u 0.164s 0:08.22 95.4% 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 13:01:09 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 !!! WARNING: HIR 137 has a net charge of 0.5140 !!! WARNING: SEP 288 has a net charge of -0.4750 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: 2.756698 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): -13.89900 44.21400 ymin,ymax (A): -24.67200 25.45500 zmin,zma (A): 21.54600 68.30400 x,y,z range (A): 58.11300 50.12700 46.75800 scale (grids/A): 2.756698 object centre (A): 15.15750 0.3915005 44.92500 number of atom coordinates read : 2785 total number of charged atoms : 2643 net assigned charge : 3.539007 assigned positive charge : 423.6803 centred at (gu) : 87.16055 86.16650 89.58231 assigned negative charge : -420.1424 centred at (gu) : 86.91506 86.68890 88.92933 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 172908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24865 grid for indexing accessible points = 1.400000 m= 83741 mr = 123830 m= 27765 mr = 66673 m= 5880 mr = 21283 m= 768 mr = 4068 m= 39 mr = 478 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.390000 number of dielectric boundary points 74757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 21135 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) : 1.837799 object centre at (A) : 15.15750 0.3915005 44.92500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0848543E-02 9.2895821E-02 midg,1,midg; midg,igrid,midg 0.2482654 7.8906327E-02 1,midg,midg; igrid,midg,midg -0.6860569 1.1685289E-02 gauss-seidel spectral radius is 0.9992440 estimated iterations to convergence 287 setup time was (sec) 1.710000 now iterating at: 13:01:11 rms-change max change #iterations 10.05649 315.9641 at 10iterations 5.951222 157.8595 at 20iterations 3.476410 77.89789 at 30iterations 2.024363 48.08721 at 40iterations 1.172157 24.84219 at 50iterations 0.6791291 12.96970 at 60iterations 0.3914979 7.707773 at 70iterations 0.2251605 4.300308 at 80iterations 0.1293456 2.422882 at 90iterations 7.4392714E-02 1.520691 at 100iterations 4.2611685E-02 0.8603802 at 110iterations 2.4403293E-02 0.4316349 at 120iterations 1.3994023E-02 0.2669106 at 130iterations 8.0076661E-03 0.1368637 at 140iterations 4.5973123E-03 8.8614464E-02 at 150iterations 2.6242726E-03 5.0121307E-02 at 160iterations 1.5046318E-03 2.6420593E-02 at 170iterations 8.6175249E-04 1.7494202E-02 at 180iterations finished qdiffx linear iterations at : 13:01:22 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 8.6175249E-04 1.7494202E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 13:01:22 12.867u 0.183s 0:13.40 97.3% 0+0k 0+0io 0pf+0w