Sat Oct 8 11:38:26 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 8 2011 at 11:38:26 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4305 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 0.5957561 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): -24.25000 35.50600 ymin,ymax (A): 36.95400 94.34300 zmin,zma (A): 30.69300 90.05600 x,y,z range (A): 59.75600 57.38900 59.36300 scale (grids/A): 0.5957561 object centre (A): 5.628000 65.64850 60.37450 number of atom coordinates read : 4305 total number of charged atoms : 4147 net assigned charge : -1.985951 assigned positive charge : 646.5005 centred at (gu) : 90.19785 88.81765 88.78968 assigned negative charge : -648.4896 centred at (gu) : 90.07784 88.96624 88.96354 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9645 nv = 96 ne = 84 npr = 91997 no. pairs analyzed = 91997 no. exposed pairs = 4670 no. arc points = 31643 no. surface atoms = 1606 nbur = 2699 mkacc time = 0.2400000 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= 456 mr = 5688 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 142 time to turn everything in is 0.4800000 number of dielectric boundary points 4355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3253 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12635 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0793884E-08 -7.8859257E-09 midg,1,midg; midg,igrid,midg 9.0116661E-09 -6.8729489E-09 1,midg,midg; igrid,midg,midg -7.1187869E-09 5.5981197E-09 gauss-seidel spectral radius is 0.9855442 estimated iterations to convergence 68 setup time was (sec) 0.8300000 now iterating at: 11:38:28 rms-change max change #iterations 0.1378176 16.13730 at 10iterations 1.1882900E-02 1.527718 at 20iterations 1.1867187E-03 0.1445637 at 30iterations 2.1572618E-04 2.7431548E-02 at 40iterations 7.0954564E-05 1.0363996E-02 at 50iterations finished qdiffx linear iterations at : 11:38:32 total time elapsed so far: 5.230000 # loops : 50 mean,max change (kT/e) : 7.0954564E-05 1.0363996E-02 energy calculations done at 5.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.400000 DelPhi exited at 11:38:33 5.403u 0.457s 0:06.24 93.7% 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 Sat Oct 8 2011 at 11:38:33 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4305 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 1.787268 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): -24.25000 35.50600 ymin,ymax (A): 36.95400 94.34300 zmin,zma (A): 30.69300 90.05600 x,y,z range (A): 59.75600 57.38900 59.36300 scale (grids/A): 1.787268 object centre (A): 5.628000 65.64850 60.37450 number of atom coordinates read : 4305 total number of charged atoms : 4147 net assigned charge : -1.985951 assigned positive charge : 646.5005 centred at (gu) : 90.59192 86.45180 86.36758 assigned negative charge : -648.4896 centred at (gu) : 90.23316 86.89835 86.89024 start vw surface at 0.1700000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 107095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31643 grid for indexing accessible points = 1.400000 m= 38181 mr = 78294 m= 5459 mr = 28952 m= 245 mr = 3565 m= 0 mr = 78 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 7300 time to turn everything in is 0.8900000 number of dielectric boundary points 40091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 32368 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) : 0.5957561 object centre at (A) : 5.628000 65.64850 60.37450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1147986E-02 -3.5044745E-02 midg,1,midg; midg,igrid,midg 3.7268989E-02 -2.4551062E-02 1,midg,midg; igrid,midg,midg -1.8752767E-02 4.6423357E-02 gauss-seidel spectral radius is 0.9985968 estimated iterations to convergence 212 setup time was (sec) 1.280000 now iterating at: 11:38:34 rms-change max change #iterations 5.019965 208.9037 at 10iterations 2.319723 70.51007 at 20iterations 1.076425 28.76178 at 30iterations 0.5004944 13.92859 at 40iterations 0.2322616 6.067230 at 50iterations 0.1080368 3.875278 at 60iterations 5.0185096E-02 1.355165 at 70iterations 2.3311233E-02 0.6559563 at 80iterations 1.0901359E-02 0.3030014 at 90iterations 5.0715944E-03 0.1290970 at 100iterations 2.3909563E-03 6.8161011E-02 at 110iterations 1.1319639E-03 3.1141937E-02 at 120iterations finished qdiffx linear iterations at : 11:38:46 total time elapsed so far: 13.00000 # loops : 120 mean,max change (kT/e) : 1.1319639E-03 3.1141937E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 11:38:47 13.160u 0.565s 0:14.35 95.6% 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 Sat Oct 8 2011 at 11:38:47 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4305 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 2.680902 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): -24.25000 35.50600 ymin,ymax (A): 36.95400 94.34300 zmin,zma (A): 30.69300 90.05600 x,y,z range (A): 59.75600 57.38900 59.36300 scale (grids/A): 2.680902 object centre (A): 5.628000 65.64850 60.37450 number of atom coordinates read : 4305 total number of charged atoms : 4147 net assigned charge : -1.985951 assigned positive charge : 646.5005 centred at (gu) : 90.88775 84.67745 84.55115 assigned negative charge : -648.4896 centred at (gu) : 90.34964 85.34753 85.33525 start vw surface at 0.1600000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 248512 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31643 grid for indexing accessible points = 1.400000 m= 126351 mr = 189330 m= 43637 mr = 105340 m= 9717 mr = 35921 m= 1179 mr = 7597 m= 37 mr = 838 m= 0 mr = 10 time to grow re-entrant surface = 1.420000 no. cavity mid-points inaccessible to solvent = 25543 time to turn everything in is 2.320000 number of dielectric boundary points 90397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.490000 number of grid points assigned charge 33167 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) : 1.787268 object centre at (A) : 5.628000 65.64850 60.37450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.177708 -0.4154097 midg,1,midg; midg,igrid,midg 0.4421106 -0.3893790 1,midg,midg; igrid,midg,midg -0.2539032 0.4580760 gauss-seidel spectral radius is 0.9992718 estimated iterations to convergence 292 setup time was (sec) 2.730000 now iterating at: 11:38:50 rms-change max change #iterations 11.94876 257.1588 at 10iterations 7.031512 139.9927 at 20iterations 4.103662 73.91785 at 30iterations 2.388579 38.70295 at 40iterations 1.391594 20.89270 at 50iterations 0.8075384 12.09737 at 60iterations 0.4683028 7.383377 at 70iterations 0.2721932 4.109601 at 80iterations 0.1572649 2.514938 at 90iterations 9.1023244E-02 1.512260 at 100iterations 5.2628968E-02 0.9068985 at 110iterations 3.0454772E-02 0.4977040 at 120iterations 1.7665658E-02 0.2900925 at 130iterations 1.0236518E-02 0.1636648 at 140iterations 5.9465226E-03 8.9782715E-02 at 150iterations 3.4629332E-03 5.4865360E-02 at 160iterations 2.0327673E-03 3.0431747E-02 at 170iterations 1.2049144E-03 1.9824982E-02 at 180iterations finished qdiffx linear iterations at : 11:39:10 total time elapsed so far: 22.93000 # loops : 180 mean,max change (kT/e) : 1.2049144E-03 1.9824982E-02 energy calculations done at 22.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.10000 DelPhi exited at 11:39:11 23.105u 0.560s 0:24.13 98.0% 0+0k 0+0io 0pf+0w