Sat Oct 8 18:29:23 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 Sat Oct 8 2011 at 18:29:23 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2425 !!! 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: ZN4 421 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6631398 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): -32.00000 17.69500 ymin,ymax (A): -23.80600 23.36000 zmin,zma (A): -12.16900 41.51500 x,y,z range (A): 49.69500 47.16600 53.68401 scale (grids/A): 0.6631398 object centre (A): -7.152500 -0.2230005 14.67300 number of atom coordinates read : 2425 total number of charged atoms : 2308 net assigned charge : 2.500008 assigned positive charge : 368.0813 centred at (gu) : 88.74259 89.19209 89.91016 assigned negative charge : -365.5818 centred at (gu) : 88.62148 89.22243 89.83109 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7225 nv = 96 ne = 84 npr = 49931 no. pairs analyzed = 49931 no. exposed pairs = 2844 no. arc points = 20463 no. surface atoms = 953 nbur = 1472 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 421 mr = 4179 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 252 time to turn everything in is 0.3800000 number of dielectric boundary points 3402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1930 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8438 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0077998E-09 2.2599679E-08 midg,1,midg; midg,igrid,midg 1.5741559E-08 9.8301156E-10 1,midg,midg; igrid,midg,midg -2.2998057E-08 2.4135801E-08 gauss-seidel spectral radius is 0.9881968 estimated iterations to convergence 75 setup time was (sec) 0.6500000 now iterating at: 18:29:24 rms-change max change #iterations 0.1621793 20.71529 at 10iterations 1.7667454E-02 2.255478 at 20iterations 1.8875245E-03 0.2747192 at 30iterations 2.0601405E-04 2.7877808E-02 at 40iterations 2.2271881E-05 3.1356812E-03 at 50iterations finished qdiffx linear iterations at : 18:29:28 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 2.2271881E-05 3.1356812E-03 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 18:29:28 4.418u 0.441s 0:05.18 93.6% 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 18:29:28 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2425 !!! 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: ZN4 421 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.989419 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): -32.00000 17.69500 ymin,ymax (A): -23.80600 23.36000 zmin,zma (A): -12.16900 41.51500 x,y,z range (A): 49.69500 47.16600 53.68401 scale (grids/A): 1.989419 object centre (A): -7.152500 -0.2230005 14.67300 number of atom coordinates read : 2425 total number of charged atoms : 2308 net assigned charge : 2.500008 assigned positive charge : 368.0813 centred at (gu) : 86.22725 87.57618 89.73026 assigned negative charge : -365.5818 centred at (gu) : 85.86420 87.66720 89.49308 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 77502 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20463 grid for indexing accessible points = 1.400000 m= 29891 mr = 54795 m= 5136 mr = 22938 m= 339 mr = 3467 m= 9 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 7173 time to turn everything in is 0.7900000 number of dielectric boundary points 31524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 18252 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) : 0.6631398 object centre at (A) : -7.152500 -0.2230005 14.67300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2541853E-02 1.4267190E-02 midg,1,midg; midg,igrid,midg 1.8931676E-02 3.3365360E-03 1,midg,midg; igrid,midg,midg -4.8686289E-03 5.0062623E-02 gauss-seidel spectral radius is 0.9987281 estimated iterations to convergence 222 setup time was (sec) 1.120000 now iterating at: 18:29:30 rms-change max change #iterations 4.447681 204.4517 at 10iterations 2.141515 68.67606 at 20iterations 1.027184 33.87988 at 30iterations 0.4945282 14.42043 at 40iterations 0.2386767 9.020256 at 50iterations 0.1145865 3.509684 at 60iterations 5.5275619E-02 1.618019 at 70iterations 2.6553566E-02 0.7726879 at 80iterations 1.2744980E-02 0.3869495 at 90iterations 6.1436105E-03 0.2108917 at 100iterations 2.9542691E-03 9.6492767E-02 at 110iterations 1.4204729E-03 4.5768738E-02 at 120iterations finished qdiffx linear iterations at : 18:29:39 total time elapsed so far: 10.06000 # loops : 120 mean,max change (kT/e) : 1.4204729E-03 4.5768738E-02 energy calculations done at 10.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.27000 DelPhi exited at 18:29:39 10.271u 0.459s 0:11.01 97.3% 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 18:29:39 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2425 !!! 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: ZN4 421 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.984129 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): -32.00000 17.69500 ymin,ymax (A): -23.80600 23.36000 zmin,zma (A): -12.16900 41.51500 x,y,z range (A): 49.69500 47.16600 53.68401 scale (grids/A): 2.984129 object centre (A): -7.152500 -0.2230005 14.67300 number of atom coordinates read : 2425 total number of charged atoms : 2308 net assigned charge : 2.500008 assigned positive charge : 368.0813 centred at (gu) : 84.34092 86.36416 89.59506 assigned negative charge : -365.5818 centred at (gu) : 83.79626 86.50067 89.23952 start vw surface at 0.1600000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 178741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20463 grid for indexing accessible points = 1.400000 m= 94988 mr = 131864 m= 36651 mr = 79695 m= 9356 mr = 30313 m= 1483 mr = 7405 m= 118 mr = 1075 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 23012 time to turn everything in is 2.090000 number of dielectric boundary points 70925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.240000 number of grid points assigned charge 18464 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) : 1.989419 object centre at (A) : -7.152500 -0.2230005 14.67300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1328142 0.1831191 midg,1,midg; midg,igrid,midg 0.2195481 -2.0287656E-03 1,midg,midg; igrid,midg,midg 6.1550196E-02 0.5782270 gauss-seidel spectral radius is 0.9992755 estimated iterations to convergence 293 setup time was (sec) 2.450000 now iterating at: 18:29:42 rms-change max change #iterations 10.15396 491.2378 at 10iterations 5.870623 120.5646 at 20iterations 3.408356 64.49793 at 30iterations 1.974870 35.69209 at 40iterations 1.140990 20.99527 at 50iterations 0.6595309 11.08918 at 60iterations 0.3820401 6.597095 at 70iterations 0.2213473 4.290106 at 80iterations 0.1277196 2.235478 at 90iterations 7.3924594E-02 1.414961 at 100iterations 4.2648718E-02 0.7301254 at 110iterations 2.4647528E-02 0.4348049 at 120iterations 1.4239324E-02 0.2427139 at 130iterations 8.2331859E-03 0.1427116 at 140iterations 4.7678505E-03 8.3557129E-02 at 150iterations 2.7553206E-03 5.0903320E-02 at 160iterations 1.5947612E-03 2.7864456E-02 at 170iterations 9.2624966E-04 1.5878856E-02 at 180iterations finished qdiffx linear iterations at : 18:29:57 total time elapsed so far: 17.38000 # loops : 180 mean,max change (kT/e) : 9.2624966E-04 1.5878856E-02 energy calculations done at 17.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.59000 DelPhi exited at 18:29:58 17.599u 0.501s 0:18.41 98.2% 0+0k 0+0io 0pf+0w