Sun Oct 9 20:05:54 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 Sun Oct 9 2011 at 20:05:54 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5118 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5465907 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): 3.355000 68.48600 ymin,ymax (A): -8.921000 53.69300 zmin,zma (A): -0.9150000 63.85900 x,y,z range (A): 65.13100 62.61400 64.77400 scale (grids/A): 0.5465907 object centre (A): 35.92050 22.38600 31.47200 number of atom coordinates read : 5118 total number of charged atoms : 4964 net assigned charge : 0.5300489 assigned positive charge : 780.1102 centred at (gu) : 87.87952 89.24843 89.08385 assigned negative charge : -779.5857 centred at (gu) : 87.76859 89.28220 89.06470 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10189 nv = 96 ne = 84 npr = 102218 no. pairs analyzed = 102218 no. exposed pairs = 6039 no. arc points = 41536 no. surface atoms = 2052 nbur = 3066 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 = 1.568000 m= 437 mr = 5847 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4227 ## 500 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 13331 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0556859E-10 2.3117032E-10 midg,1,midg; midg,igrid,midg 5.5835181E-10 -2.7874889E-10 1,midg,midg; igrid,midg,midg -2.1763729E-09 8.0307772E-10 gauss-seidel spectral radius is 0.9829028 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 20:05:55 rms-change max change #iterations 0.1048599 14.40872 at 10iterations 1.2526091E-02 1.573532 at 20iterations 5.0511151E-03 0.7367973 at 30iterations 2.4555463E-03 0.3669930 at 40iterations 1.2039440E-03 0.1805840 at 50iterations finished qdiffx linear iterations at : 20:05:58 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.2039440E-03 0.1805840 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 20:05:58 3.578u 0.205s 0:04.14 91.0% 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 20:05:58 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5118 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.639772 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): 3.355000 68.48600 ymin,ymax (A): -8.921000 53.69300 zmin,zma (A): -0.9150000 63.85900 x,y,z range (A): 65.13100 62.61400 64.77400 scale (grids/A): 1.639772 object centre (A): 35.92050 22.38600 31.47200 number of atom coordinates read : 5118 total number of charged atoms : 4964 net assigned charge : 0.5300489 assigned positive charge : 780.1102 centred at (gu) : 83.63732 87.74374 87.25038 assigned negative charge : -779.5857 centred at (gu) : 83.30576 87.84628 87.19407 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 114353 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 39579 mr = 82994 m= 4656 mr = 28786 m= 142 mr = 2488 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.5600000 number of dielectric boundary points 44438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 416 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 38064 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) : 0.5465907 object centre at (A) : 35.92050 22.38600 31.47200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2936398E-02 -1.2701410E-02 midg,1,midg; midg,igrid,midg 2.0490214E-02 9.3622040E-03 1,midg,midg; igrid,midg,midg -2.0054337E-02 1.8287798E-02 gauss-seidel spectral radius is 0.9984021 estimated iterations to convergence 199 setup time was (sec) 0.7800000 now iterating at: 20:05:59 rms-change max change #iterations 4.704528 179.6796 at 10iterations 2.067489 60.95792 at 20iterations 0.9145826 26.44250 at 30iterations 0.4034664 10.49168 at 40iterations 0.1789559 4.854172 at 50iterations 8.0113746E-02 2.591179 at 60iterations 3.7108649E-02 1.091232 at 70iterations 1.8345905E-02 0.5595245 at 80iterations 1.0452260E-02 0.3391724 at 90iterations 6.8113948E-03 0.2114410 at 100iterations 4.8890756E-03 0.1467056 at 110iterations 3.6864693E-03 0.1084251 at 120iterations finished qdiffx linear iterations at : 20:06:07 total time elapsed so far: 8.330000 # loops : 120 mean,max change (kT/e) : 3.6864693E-03 0.1084251 energy calculations done at 8.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.460000 DelPhi exited at 20:06:08 8.461u 0.780s 0:09.54 96.8% 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 Sun Oct 9 2011 at 20:06:08 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5118 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.459658 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): 3.355000 68.48600 ymin,ymax (A): -8.921000 53.69300 zmin,zma (A): -0.9150000 63.85900 x,y,z range (A): 65.13100 62.61400 64.77400 scale (grids/A): 2.459658 object centre (A): 35.92050 22.38600 31.47200 number of atom coordinates read : 5118 total number of charged atoms : 4964 net assigned charge : 0.5300489 assigned positive charge : 780.1102 centred at (gu) : 80.45568 86.61530 85.87518 assigned negative charge : -779.5857 centred at (gu) : 79.95853 86.76958 85.79116 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 265874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 134658 mr = 201968 m= 41489 mr = 110136 m= 7511 mr = 32279 m= 597 mr = 5192 m= 12 mr = 337 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 337 time to turn everything in is 1.460000 number of dielectric boundary points 100229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 39667 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) : 1.639772 object centre at (A) : 35.92050 22.38600 31.47200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5056329 -0.2660331 midg,1,midg; midg,igrid,midg 0.1957141 2.8296899E-02 1,midg,midg; igrid,midg,midg -0.4867119 0.2651232 gauss-seidel spectral radius is 0.9992480 estimated iterations to convergence 288 setup time was (sec) 1.710000 now iterating at: 20:06:10 rms-change max change #iterations 11.97145 318.1942 at 10iterations 7.044638 136.5506 at 20iterations 4.110912 82.44592 at 30iterations 2.391565 53.51218 at 40iterations 1.387328 28.02220 at 50iterations 0.8020548 15.16299 at 60iterations 0.4638115 8.169025 at 70iterations 0.2676998 4.433353 at 80iterations 0.1543343 2.539836 at 90iterations 8.9194328E-02 1.680023 at 100iterations 5.1756658E-02 0.8240318 at 110iterations 3.0478036E-02 0.5111389 at 120iterations 1.8353483E-02 0.3714848 at 130iterations 1.1536305E-02 0.2021103 at 140iterations 7.7211233E-03 0.1370621 at 150iterations 5.5798786E-03 0.1149788 at 160iterations 4.3057646E-03 8.0692291E-02 at 170iterations 3.4706104E-03 6.3312531E-02 at 180iterations finished qdiffx linear iterations at : 20:06:22 total time elapsed so far: 13.87000 # loops : 180 mean,max change (kT/e) : 3.4706104E-03 6.3312531E-02 energy calculations done at 13.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.01000 DelPhi exited at 20:06:22 14.013u 0.266s 0:14.76 96.6% 0+0k 0+0io 0pf+0w