Mon Oct 10 14:01:02 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 Mon Oct 10 2011 at 14:01:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 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: 0.5844593 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): 50.13600 111.0470 ymin,ymax (A): -18.87000 40.84000 zmin,zma (A): -34.47900 24.47900 x,y,z range (A): 60.91100 59.71000 58.95800 scale (grids/A): 0.5844593 object centre (A): 80.59150 10.98500 -5.000000 number of atom coordinates read : 3253 total number of charged atoms : 3111 net assigned charge : 5.500040 assigned positive charge : 483.5617 centred at (gu) : 88.20359 89.85661 91.49518 assigned negative charge : -478.0631 centred at (gu) : 88.14411 90.02734 91.44765 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7440 nv = 96 ne = 84 npr = 65061 no. pairs analyzed = 65061 no. exposed pairs = 4321 no. arc points = 30274 no. surface atoms = 1424 nbur = 1829 mkacc time = 0.1400000 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= 384 mr = 3831 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3700000 number of dielectric boundary points 3971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3038 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9442 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7276464E-11 3.8088817E-09 midg,1,midg; midg,igrid,midg 6.1636123E-09 -3.2309129E-09 1,midg,midg; igrid,midg,midg -4.0009285E-10 1.9961164E-09 gauss-seidel spectral radius is 0.9849194 estimated iterations to convergence 67 setup time was (sec) 0.6000000 now iterating at: 14:01:04 rms-change max change #iterations 0.1064980 15.69751 at 10iterations 9.1038821E-03 1.266865 at 20iterations 1.1898656E-03 0.1673584 at 30iterations 2.9586145E-04 4.3869019E-02 at 40iterations 8.4867526E-05 1.2687683E-02 at 50iterations finished qdiffx linear iterations at : 14:01:06 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 8.4867526E-05 1.2687683E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:01:07 3.390u 0.251s 0:04.50 80.8% 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 Mon Oct 10 2011 at 14:01:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 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: 1.753378 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): 50.13600 111.0470 ymin,ymax (A): -18.87000 40.84000 zmin,zma (A): -34.47900 24.47900 x,y,z range (A): 60.91100 59.71000 58.95800 scale (grids/A): 1.753378 object centre (A): 80.59150 10.98500 -5.000000 number of atom coordinates read : 3253 total number of charged atoms : 3111 net assigned charge : 5.500040 assigned positive charge : 483.5617 centred at (gu) : 84.60970 89.56907 94.48454 assigned negative charge : -478.0631 centred at (gu) : 84.43194 90.08180 94.34256 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 81413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30274 grid for indexing accessible points = 1.400000 m= 28344 mr = 54827 m= 3985 mr = 19956 m= 138 mr = 2330 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 247 time to turn everything in is 0.6000000 number of dielectric boundary points 36737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 24217 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) : 0.5844593 object centre at (A) : 80.59150 10.98500 -5.000000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8192450E-03 3.0346667E-02 midg,1,midg; midg,igrid,midg 2.0622730E-02 -2.5239129E-02 1,midg,midg; igrid,midg,midg 1.1720476E-03 5.8019413E-03 gauss-seidel spectral radius is 0.9984658 estimated iterations to convergence 203 setup time was (sec) 0.9000000 now iterating at: 14:01:09 rms-change max change #iterations 4.057419 157.9629 at 10iterations 1.806477 58.58895 at 20iterations 0.8066073 29.22503 at 30iterations 0.3598572 12.56144 at 40iterations 0.1611708 4.936322 at 50iterations 7.2354741E-02 2.126923 at 60iterations 3.2448031E-02 1.075609 at 70iterations 1.4582403E-02 0.4515457 at 80iterations 6.6353572E-03 0.2105942 at 90iterations 3.0487080E-03 9.6708298E-02 at 100iterations 1.4382261E-03 5.0800323E-02 at 110iterations 7.0679368E-04 2.3994446E-02 at 120iterations finished qdiffx linear iterations at : 14:01:15 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 7.0679368E-04 2.3994446E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 14:01:16 7.643u 0.255s 0:08.34 94.6% 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 Mon Oct 10 2011 at 14:01:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 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: 2.630067 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): 50.13600 111.0470 ymin,ymax (A): -18.87000 40.84000 zmin,zma (A): -34.47900 24.47900 x,y,z range (A): 60.91100 59.71000 58.95800 scale (grids/A): 2.630067 object centre (A): 80.59150 10.98500 -5.000000 number of atom coordinates read : 3253 total number of charged atoms : 3111 net assigned charge : 5.500040 assigned positive charge : 483.5617 centred at (gu) : 81.91436 89.35352 96.72652 assigned negative charge : -478.0631 centred at (gu) : 81.64802 90.12260 96.51386 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 188633 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30274 grid for indexing accessible points = 1.400000 m= 92347 mr = 134042 m= 31971 mr = 73379 m= 6957 mr = 24997 m= 673 mr = 5015 m= 21 mr = 350 m= 0 mr = 12 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 866 time to turn everything in is 1.480000 number of dielectric boundary points 82807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 24880 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) : 1.753378 object centre at (A) : 80.59150 10.98500 -5.000000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1325908 0.2353919 midg,1,midg; midg,igrid,midg 0.2729267 -0.3235240 1,midg,midg; igrid,midg,midg 0.3324706 2.4769974E-03 gauss-seidel spectral radius is 0.9992318 estimated iterations to convergence 285 setup time was (sec) 1.790000 now iterating at: 14:01:18 rms-change max change #iterations 10.10221 317.5184 at 10iterations 5.956943 170.8105 at 20iterations 3.472891 82.87440 at 30iterations 2.019186 41.39631 at 40iterations 1.166730 22.68304 at 50iterations 0.6742146 14.35807 at 60iterations 0.3862027 8.561769 at 70iterations 0.2218333 3.967584 at 80iterations 0.1270305 2.914612 at 90iterations 7.2648607E-02 1.491409 at 100iterations 4.1445240E-02 0.8144760 at 110iterations 2.3690993E-02 0.4668007 at 120iterations 1.3526690E-02 0.2439299 at 130iterations 7.7166627E-03 0.1357689 at 140iterations 4.4249790E-03 9.1186047E-02 at 150iterations 2.5405528E-03 5.1612854E-02 at 160iterations 1.4622567E-03 2.9472351E-02 at 170iterations 8.4936776E-04 1.5262604E-02 at 180iterations finished qdiffx linear iterations at : 14:01:30 total time elapsed so far: 14.07000 # loops : 180 mean,max change (kT/e) : 8.4936776E-04 1.5262604E-02 energy calculations done at 14.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.25000 DelPhi exited at 14:01:31 14.253u 0.277s 0:15.56 93.3% 0+0k 0+0io 0pf+0w