Wed Dec 28 11:01:34 PST 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 Wed Dec 28 2011 at 11:01:34 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 = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5687718 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): -34.52200 12.60100 ymin,ymax (A): 0.3030000 41.35100 zmin,zma (A): -1.518000 61.07300 x,y,z range (A): 47.12300 41.04800 62.59100 scale (grids/A): 0.5687718 object centre (A): -10.96050 20.82700 29.77750 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 285.3841 centred at (gu) : 89.54212 89.81728 88.86636 assigned negative charge : -281.3843 centred at (gu) : 89.42459 90.00578 88.84597 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4277 nv = 96 ne = 84 npr = 39540 no. pairs analyzed = 39540 no. exposed pairs = 2415 no. arc points = 17400 no. surface atoms = 823 nbur = 1125 mkacc time = 0.1000000 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 = 1.540000 m= 200 mr = 2299 m= 0 mr = 18 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1808 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 5382 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1568433E-10 6.0488098E-10 midg,1,midg; midg,igrid,midg 2.4531990E-09 -1.1881025E-09 1,midg,midg; igrid,midg,midg -6.0940758E-10 1.5217301E-09 gauss-seidel spectral radius is 0.9839686 estimated iterations to convergence 65 setup time was (sec) 0.6000000 now iterating at: 11:01:46 rms-change max change #iterations 6.9649294E-02 13.34473 at 10iterations 5.3256489E-03 0.8700485 at 20iterations 3.8623094E-04 6.9187164E-02 at 30iterations 2.8593475E-05 5.0506592E-03 at 40iterations 2.1294404E-06 3.7384033E-04 at 50iterations finished qdiffx linear iterations at : 11:01:52 total time elapsed so far: 7.160000 # loops : 50 mean,max change (kT/e) : 2.1294404E-06 3.7384033E-04 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 11:01:53 7.333u 0.711s 0:18.61 43.2% 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 Wed Dec 28 2011 at 11:01:53 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 = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.706316 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): -34.52200 12.60100 ymin,ymax (A): 0.3030000 41.35100 zmin,zma (A): -1.518000 61.07300 x,y,z range (A): 47.12300 41.04800 62.59100 scale (grids/A): 1.706316 object centre (A): -10.96050 20.82700 29.77750 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 285.3841 centred at (gu) : 88.62643 89.45196 86.59910 assigned negative charge : -281.3843 centred at (gu) : 88.27403 90.01742 86.53821 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 46827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17400 grid for indexing accessible points = 1.400000 m= 16033 mr = 32006 m= 2056 mr = 11909 m= 90 mr = 1229 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 248 time to turn everything in is 0.5200000 number of dielectric boundary points 19848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 14064 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) : 0.5687718 object centre at (A) : -10.96050 20.82700 29.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3028590E-02 1.7127195E-02 midg,1,midg; midg,igrid,midg 8.4573505E-03 -8.0890171E-03 1,midg,midg; igrid,midg,midg -2.6064764E-03 1.2472942E-03 gauss-seidel spectral radius is 0.9982229 estimated iterations to convergence 188 setup time was (sec) 1.030000 now iterating at: 11:02:05 rms-change max change #iterations 2.825752 167.7493 at 10iterations 1.185548 63.00649 at 20iterations 0.4985515 23.84235 at 30iterations 0.2102786 8.803864 at 40iterations 8.8458396E-02 4.078651 at 50iterations 3.7156478E-02 1.496095 at 60iterations 1.5613897E-02 0.6336498 at 70iterations 6.5546436E-03 0.2636185 at 80iterations 2.7698989E-03 0.1105680 at 90iterations 1.1636561E-03 4.8240662E-02 at 100iterations 4.8824144E-04 1.8411636E-02 at 110iterations 2.0663292E-04 8.2798004E-03 at 120iterations finished qdiffx linear iterations at : 11:02:22 total time elapsed so far: 18.61000 # loops : 120 mean,max change (kT/e) : 2.0663292E-04 8.2798004E-03 energy calculations done at 18.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.79000 DelPhi exited at 11:02:23 18.793u 0.918s 0:30.42 64.7% 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 Wed Dec 28 2011 at 11:02:23 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 = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.559473 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): -34.52200 12.60100 ymin,ymax (A): 0.3030000 41.35100 zmin,zma (A): -1.518000 61.07300 x,y,z range (A): 47.12300 41.04800 62.59100 scale (grids/A): 2.559473 object centre (A): -10.96050 20.82700 29.77750 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 285.3841 centred at (gu) : 87.93950 89.17796 84.89869 assigned negative charge : -281.3843 centred at (gu) : 87.41113 90.02627 84.80739 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 108290 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17400 grid for indexing accessible points = 1.400000 m= 53504 mr = 77384 m= 17573 mr = 43925 m= 3357 mr = 14257 m= 354 mr = 2455 m= 8 mr = 229 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 837 time to turn everything in is 1.110000 number of dielectric boundary points 44836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 14538 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) : 1.706316 object centre at (A) : -10.96050 20.82700 29.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2536717 0.1745066 midg,1,midg; midg,igrid,midg 8.5292295E-02 -0.1218555 1,midg,midg; igrid,midg,midg -4.2724051E-02 2.1515477E-02 gauss-seidel spectral radius is 0.9991149 estimated iterations to convergence 266 setup time was (sec) 1.690000 now iterating at: 11:02:34 rms-change max change #iterations 6.939642 321.9777 at 10iterations 3.812921 91.14244 at 20iterations 2.075207 54.41411 at 30iterations 1.127592 28.54535 at 40iterations 0.6131185 14.99858 at 50iterations 0.3342268 8.332842 at 60iterations 0.1820689 4.902863 at 70iterations 9.8675087E-02 2.501911 at 80iterations 5.3716872E-02 1.212111 at 90iterations 2.9179910E-02 0.6746693 at 100iterations 1.5891897E-02 0.3573661 at 110iterations 8.6115310E-03 0.2080488 at 120iterations 4.6872767E-03 0.1045775 at 130iterations 2.5456578E-03 5.6042671E-02 at 140iterations 1.3871324E-03 3.2744408E-02 at 150iterations 7.5415394E-04 1.6883373E-02 at 160iterations 4.1097534E-04 9.8934174E-03 at 170iterations 2.2210712E-04 5.3443909E-03 at 180iterations finished qdiffx linear iterations at : 11:03:02 total time elapsed so far: 29.68000 # loops : 180 mean,max change (kT/e) : 2.2210712E-04 5.3443909E-03 energy calculations done at 29.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.85000 DelPhi exited at 11:03:03 29.858u 0.815s 0:39.78 77.0% 0+0k 0+0io 0pf+0w