Tue Oct 11 05:52:15 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 05:52:15 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2330 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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: 0.7077394 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): 25.63300 72.12100 ymin,ymax (A): -18.71800 31.58300 zmin,zma (A): 3.957000 46.35300 x,y,z range (A): 46.48800 50.30100 42.39600 scale (grids/A): 0.7077394 object centre (A): 48.87700 6.432500 25.15500 number of atom coordinates read : 2330 total number of charged atoms : 1999 net assigned charge : 5.945011 assigned positive charge : 328.1329 centred at (gu) : 89.28494 90.22515 90.36362 assigned negative charge : -322.1880 centred at (gu) : 89.41210 90.15948 90.44686 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7264 nv = 96 ne = 84 npr = 42811 no. pairs analyzed = 42811 no. exposed pairs = 2609 no. arc points = 17680 no. surface atoms = 892 nbur = 1438 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 481 mr = 4208 m= 3 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1614 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7975 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6305178E-08 7.2845858E-09 midg,1,midg; midg,igrid,midg 1.5579417E-08 8.7388365E-08 1,midg,midg; igrid,midg,midg 1.3186154E-07 -1.3555202E-08 gauss-seidel spectral radius is 0.9895964 estimated iterations to convergence 80 setup time was (sec) 0.6100000 now iterating at: 05:52:16 rms-change max change #iterations 0.2055761 28.37247 at 10iterations 2.6009316E-02 3.734608 at 20iterations 3.5476203E-03 0.4576797 at 30iterations 6.4890651E-04 8.6830139E-02 at 40iterations 1.7897197E-04 2.1074295E-02 at 50iterations finished qdiffx linear iterations at : 05:52:19 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 1.7897197E-04 2.1074295E-02 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 05:52:20 4.112u 0.239s 0:04.97 87.3% 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 05:52:20 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2330 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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: 2.123218 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): 25.63300 72.12100 ymin,ymax (A): -18.71800 31.58300 zmin,zma (A): 3.957000 46.35300 x,y,z range (A): 46.48800 50.30100 42.39600 scale (grids/A): 2.123218 object centre (A): 48.87700 6.432500 25.15500 number of atom coordinates read : 2330 total number of charged atoms : 1999 net assigned charge : 5.945011 assigned positive charge : 328.1329 centred at (gu) : 87.85475 90.67527 91.09074 assigned negative charge : -322.1880 centred at (gu) : 88.23628 90.47851 91.34067 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17680 grid for indexing accessible points = 1.400000 m= 31489 mr = 54750 m= 6095 mr = 23985 m= 555 mr = 4087 m= 18 mr = 264 m= 0 mr = 9 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 31757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 15854 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) : 0.7077394 object centre at (A) : 48.87700 6.432500 25.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1369999E-02 2.8857356E-02 midg,1,midg; midg,igrid,midg 3.9737295E-02 2.7336420E-02 1,midg,midg; igrid,midg,midg 4.3833736E-02 -4.8144545E-02 gauss-seidel spectral radius is 0.9988360 estimated iterations to convergence 232 setup time was (sec) 1.020000 now iterating at: 05:52:21 rms-change max change #iterations 4.707663 218.1635 at 10iterations 2.333630 78.15018 at 20iterations 1.161424 37.06508 at 30iterations 0.5768803 16.22521 at 40iterations 0.2875946 8.208296 at 50iterations 0.1429030 4.425392 at 60iterations 7.1099661E-02 2.135822 at 70iterations 3.5409618E-02 1.086664 at 80iterations 1.7807983E-02 0.5713348 at 90iterations 8.9609008E-03 0.2715673 at 100iterations 4.5408430E-03 0.1432724 at 110iterations 2.3816200E-03 6.9629192E-02 at 120iterations finished qdiffx linear iterations at : 05:52:30 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 2.3816200E-03 6.9629192E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 05:52:30 9.649u 0.321s 0:10.44 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 Tue Oct 11 2011 at 05:52:30 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2330 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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: 3.184827 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): 25.63300 72.12100 ymin,ymax (A): -18.71800 31.58300 zmin,zma (A): 3.957000 46.35300 x,y,z range (A): 46.48800 50.30100 42.39600 scale (grids/A): 3.184827 object centre (A): 48.87700 6.432500 25.15500 number of atom coordinates read : 2330 total number of charged atoms : 1999 net assigned charge : 5.945011 assigned positive charge : 328.1329 centred at (gu) : 86.78207 91.01302 91.63609 assigned negative charge : -322.1880 centred at (gu) : 87.35435 90.71778 92.01096 start vw surface at 0.1600000 fill in re-entrant regions at 1.020000 boundary points on vw surface= 176481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17680 grid for indexing accessible points = 1.400000 m= 97405 mr = 131636 m= 40288 mr = 81327 m= 11602 mr = 33055 m= 2279 mr = 9011 m= 267 mr = 1633 m= 14 mr = 166 m= 0 mr = 2 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.320000 number of dielectric boundary points 71506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.490000 number of grid points assigned charge 15992 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) : 2.123218 object centre at (A) : 48.87700 6.432500 25.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1388542 0.2447283 midg,1,midg; midg,igrid,midg 0.2871212 0.1171325 1,midg,midg; igrid,midg,midg 0.4333404 -0.6068835 gauss-seidel spectral radius is 0.9992989 estimated iterations to convergence 298 setup time was (sec) 2.660000 now iterating at: 05:52:33 rms-change max change #iterations 10.48938 369.8242 at 10iterations 6.218801 170.4948 at 20iterations 3.679728 76.39631 at 30iterations 2.173647 38.55747 at 40iterations 1.277857 23.10169 at 50iterations 0.7523237 15.22909 at 60iterations 0.4421060 8.313787 at 70iterations 0.2597772 5.214903 at 80iterations 0.1523833 3.156353 at 90iterations 8.9660734E-02 1.720036 at 100iterations 5.2738167E-02 0.9395819 at 110iterations 3.1140389E-02 0.5354271 at 120iterations 1.8546747E-02 0.3341751 at 130iterations 1.1215113E-02 0.2130013 at 140iterations 6.9440487E-03 0.1367455 at 150iterations 4.4550779E-03 8.8775635E-02 at 160iterations 3.0239394E-03 6.2774658E-02 at 170iterations 2.1676351E-03 4.4311523E-02 at 180iterations finished qdiffx linear iterations at : 05:52:47 total time elapsed so far: 16.63000 # loops : 180 mean,max change (kT/e) : 2.1676351E-03 4.4311523E-02 energy calculations done at 16.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.81000 DelPhi exited at 05:52:48 16.814u 0.298s 0:17.69 96.6% 0+0k 0+0io 0pf+0w