Sun Oct 9 23:37:08 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 Sun Oct 9 2011 at 23:37:08 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 !!! WARNING: SEP 137 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5874296 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): -25.06800 30.87900 ymin,ymax (A): -27.02600 26.59300 zmin,zma (A): -9.301000 51.30200 x,y,z range (A): 55.94700 53.61900 60.60300 scale (grids/A): 0.5874296 object centre (A): 2.905500 -0.2165003 21.00050 number of atom coordinates read : 3656 total number of charged atoms : 3538 net assigned charge : -2.974987 assigned positive charge : 565.9733 centred at (gu) : 89.39704 90.35032 89.94462 assigned negative charge : -568.9510 centred at (gu) : 89.47008 90.42087 89.95797 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8500 nv = 96 ne = 84 npr = 69175 no. pairs analyzed = 69175 no. exposed pairs = 5190 no. arc points = 37338 no. surface atoms = 1682 nbur = 1974 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 398 mr = 4180 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3755 ## 412 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10865 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7099609E-10 -1.3099640E-09 midg,1,midg; midg,igrid,midg 1.5340526E-09 -3.6933867E-09 1,midg,midg; igrid,midg,midg 2.0332609E-09 -3.0378455E-09 gauss-seidel spectral radius is 0.9851090 estimated iterations to convergence 67 setup time was (sec) 0.6200000 now iterating at: 23:37:09 rms-change max change #iterations 0.1183215 15.52836 at 10iterations 9.5851040E-03 1.300644 at 20iterations 9.2401553E-04 0.1192358 at 30iterations 2.0557562E-04 2.0927429E-02 at 40iterations 7.8305369E-05 7.8692436E-03 at 50iterations finished qdiffx linear iterations at : 23:37:12 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 7.8305369E-05 7.8692436E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 23:37:12 3.394u 0.148s 0:03.82 92.4% 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 Sun Oct 9 2011 at 23:37:12 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 !!! WARNING: SEP 137 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.762289 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): -25.06800 30.87900 ymin,ymax (A): -27.02600 26.59300 zmin,zma (A): -9.301000 51.30200 x,y,z range (A): 55.94700 53.61900 60.60300 scale (grids/A): 1.762289 object centre (A): 2.905500 -0.2165003 21.00050 number of atom coordinates read : 3656 total number of charged atoms : 3538 net assigned charge : -2.974987 assigned positive charge : 565.9733 centred at (gu) : 88.18999 91.04969 89.83266 assigned negative charge : -568.9510 centred at (gu) : 88.40971 91.26230 89.87366 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 92755 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37338 grid for indexing accessible points = 1.400000 m= 30101 mr = 61080 m= 3759 mr = 20161 m= 164 mr = 1859 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 486 time to turn everything in is 0.6600000 number of dielectric boundary points 43648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 27575 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) : 0.5874296 object centre at (A) : 2.905500 -0.2165003 21.00050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7408684E-03 -3.2939710E-02 midg,1,midg; midg,igrid,midg 1.3982449E-02 -1.0800107E-02 1,midg,midg; igrid,midg,midg 9.5688812E-03 -5.0266129E-03 gauss-seidel spectral radius is 0.9985508 estimated iterations to convergence 208 setup time was (sec) 0.9500000 now iterating at: 23:37:13 rms-change max change #iterations 4.529217 170.5345 at 10iterations 2.053632 72.41074 at 20iterations 0.9378221 29.21848 at 30iterations 0.4267556 13.67647 at 40iterations 0.1941963 6.168404 at 50iterations 8.8748246E-02 2.576419 at 60iterations 4.0589727E-02 1.259373 at 70iterations 1.8582242E-02 0.5508194 at 80iterations 8.4956596E-03 0.2663507 at 90iterations 3.9090780E-03 0.1172168 at 100iterations 1.8133908E-03 6.3675880E-02 at 110iterations 8.5369288E-04 2.6935577E-02 at 120iterations finished qdiffx linear iterations at : 23:37:20 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 8.5369288E-04 2.6935577E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 23:37:21 7.642u 0.166s 0:08.17 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 Sun Oct 9 2011 at 23:37:21 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 !!! WARNING: SEP 137 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.643434 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): -25.06800 30.87900 ymin,ymax (A): -27.02600 26.59300 zmin,zma (A): -9.301000 51.30200 x,y,z range (A): 55.94700 53.61900 60.60300 scale (grids/A): 2.643434 object centre (A): 2.905500 -0.2165003 21.00050 number of atom coordinates read : 3656 total number of charged atoms : 3538 net assigned charge : -2.974987 assigned positive charge : 565.9733 centred at (gu) : 87.28461 91.57420 89.74879 assigned negative charge : -568.9510 centred at (gu) : 87.61459 91.89333 89.81037 start vw surface at 0.2400000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 214671 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37338 grid for indexing accessible points = 1.400000 m= 101026 mr = 149602 m= 31334 mr = 78508 m= 6138 mr = 22925 m= 709 mr = 3963 m= 35 mr = 394 m= 0 mr = 3 time to grow re-entrant surface = 0.9900001 no. cavity mid-points inaccessible to solvent = 1868 time to turn everything in is 1.720000 number of dielectric boundary points 98518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 28294 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) : 1.762289 object centre at (A) : 2.905500 -0.2165003 21.00050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1130786 -0.4900046 midg,1,midg; midg,igrid,midg 0.1775192 -0.1263476 1,midg,midg; igrid,midg,midg 9.0507030E-02 -1.8988881E-02 gauss-seidel spectral radius is 0.9992835 estimated iterations to convergence 295 setup time was (sec) 2.030000 now iterating at: 23:37:23 rms-change max change #iterations 11.43359 332.9644 at 10iterations 6.954350 178.5728 at 20iterations 4.186381 92.58093 at 30iterations 2.497066 47.65750 at 40iterations 1.482046 30.74598 at 50iterations 0.8778981 19.50409 at 60iterations 0.5170360 10.81838 at 70iterations 0.3037144 5.731832 at 80iterations 0.1787965 3.415751 at 90iterations 0.1048376 1.994202 at 100iterations 6.1273728E-02 1.102355 at 110iterations 3.5835810E-02 0.6281204 at 120iterations 2.0898284E-02 0.4009094 at 130iterations 1.2217630E-02 0.2128448 at 140iterations 7.1292408E-03 0.1272697 at 150iterations 4.1682622E-03 8.3084106E-02 at 160iterations 2.4319466E-03 4.4118881E-02 at 170iterations 1.4281586E-03 2.7450562E-02 at 180iterations finished qdiffx linear iterations at : 23:37:34 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 1.4281586E-03 2.7450562E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 23:37:34 13.429u 0.182s 0:13.90 97.8% 0+0k 0+0io 0pf+0w