Sat Oct 8 19:18:54 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+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 19:18:54 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 901 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6283424 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): -31.81300 17.69900 ymin,ymax (A): -23.75600 22.90300 zmin,zma (A): -12.33300 44.32400 x,y,z range (A): 49.51200 46.65900 56.65700 scale (grids/A): 0.6283424 object centre (A): -7.057000 -0.4265003 15.99550 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 394.2351 centred at (gu) : 88.60730 89.28984 89.84026 assigned negative charge : -389.8296 centred at (gu) : 88.50723 89.33485 89.73715 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6796 nv = 96 ne = 84 npr = 54627 no. pairs analyzed = 54627 no. exposed pairs = 2978 no. arc points = 21565 no. surface atoms = 1005 nbur = 1597 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 338 mr = 3848 m= 4 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 117 time to turn everything in is 0.3400000 number of dielectric boundary points 3241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2111 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8237 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2992454E-09 1.2844759E-08 midg,1,midg; midg,igrid,midg 9.8734478E-09 7.6206014E-10 1,midg,midg; igrid,midg,midg -5.4025602E-09 9.6600452E-09 gauss-seidel spectral radius is 0.9868764 estimated iterations to convergence 71 setup time was (sec) 0.5800000 now iterating at: 19:18:55 rms-change max change #iterations 0.1382809 19.61134 at 10iterations 1.3274283E-02 2.333588 at 20iterations 1.2500332E-03 0.1863518 at 30iterations 1.1884451E-04 1.6269684E-02 at 40iterations 1.1485950E-05 1.6555786E-03 at 50iterations finished qdiffx linear iterations at : 19:18:57 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.1485950E-05 1.6555786E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 19:18:58 3.364u 0.207s 0:03.87 91.9% 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 19:18:58 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 901 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.885027 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): -31.81300 17.69900 ymin,ymax (A): -23.75600 22.90300 zmin,zma (A): -12.33300 44.32400 x,y,z range (A): 49.51200 46.65900 56.65700 scale (grids/A): 1.885027 object centre (A): -7.057000 -0.4265003 15.99550 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 394.2351 centred at (gu) : 85.82115 87.86961 89.52027 assigned negative charge : -389.8296 centred at (gu) : 85.52134 88.00436 89.21115 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 73278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21565 grid for indexing accessible points = 1.400000 m= 26578 mr = 51518 m= 4105 mr = 20153 m= 191 mr = 2635 m= 0 mr = 50 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 5265 time to turn everything in is 0.5700000 number of dielectric boundary points 29796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19355 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) : 0.6283424 object centre at (A) : -7.057000 -0.4265003 15.99550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2470420E-02 3.1454153E-02 midg,1,midg; midg,igrid,midg 1.6811837E-02 3.2610502E-03 1,midg,midg; igrid,midg,midg -4.4930084E-03 4.0004931E-02 gauss-seidel spectral radius is 0.9986034 estimated iterations to convergence 212 setup time was (sec) 0.8800000 now iterating at: 19:18:59 rms-change max change #iterations 4.169902 194.8327 at 10iterations 1.932859 69.81652 at 20iterations 0.8973649 30.10350 at 30iterations 0.4155618 13.20528 at 40iterations 0.1937172 6.182823 at 50iterations 8.9946449E-02 2.834694 at 60iterations 4.1883491E-02 1.406128 at 70iterations 1.9409573E-02 0.6403008 at 80iterations 9.0219611E-03 0.2748260 at 90iterations 4.1796681E-03 0.1386604 at 100iterations 1.9502438E-03 6.4228058E-02 at 110iterations 9.0540387E-04 2.9918671E-02 at 120iterations finished qdiffx linear iterations at : 19:19:06 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 9.0540387E-04 2.9918671E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 19:19:06 7.613u 0.218s 0:08.11 96.4% 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 Sat Oct 8 2011 at 19:19:06 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 901 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.827541 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): -31.81300 17.69900 ymin,ymax (A): -23.75600 22.90300 zmin,zma (A): -12.33300 44.32400 x,y,z range (A): 49.51200 46.65900 56.65700 scale (grids/A): 2.827541 object centre (A): -7.057000 -0.4265003 15.99550 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 394.2351 centred at (gu) : 83.73171 86.80431 89.28035 assigned negative charge : -389.8296 centred at (gu) : 83.28210 87.00661 88.81671 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 169412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21565 grid for indexing accessible points = 1.400000 m= 86786 mr = 124629 m= 31133 mr = 72235 m= 7220 mr = 25455 m= 934 mr = 5520 m= 41 mr = 623 m= 0 mr = 12 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 17387 time to turn everything in is 1.310000 number of dielectric boundary points 67052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 19695 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) : 1.885027 object centre at (A) : -7.057000 -0.4265003 15.99550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1636406 0.4101358 midg,1,midg; midg,igrid,midg 0.1939674 1.9304188E-02 1,midg,midg; igrid,midg,midg 1.6299500E-03 0.5046965 gauss-seidel spectral radius is 0.9992439 estimated iterations to convergence 287 setup time was (sec) 1.650000 now iterating at: 19:19:08 rms-change max change #iterations 9.697771 345.3686 at 10iterations 5.586529 105.7789 at 20iterations 3.206357 82.38261 at 30iterations 1.831686 32.35420 at 40iterations 1.047897 20.59460 at 50iterations 0.5976032 11.27788 at 60iterations 0.3417032 6.148621 at 70iterations 0.1952429 3.572746 at 80iterations 0.1114796 1.964489 at 90iterations 6.3528828E-02 1.107178 at 100iterations 3.6353901E-02 0.7221661 at 110iterations 2.0728402E-02 0.3854052 at 120iterations 1.1820965E-02 0.2197266 at 130iterations 6.7433654E-03 0.1243398 at 140iterations 3.8469899E-03 6.7962646E-02 at 150iterations 2.1918286E-03 4.2409897E-02 at 160iterations 1.2536953E-03 2.2751331E-02 at 170iterations 7.1522815E-04 1.3854980E-02 at 180iterations finished qdiffx linear iterations at : 19:19:18 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 7.1522815E-04 1.3854980E-02 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 19:19:19 12.176u 0.230s 0:12.76 97.1% 0+0k 0+0io 0pf+0w