Wed Dec 28 11:01:30 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 11:01:30 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 0.6546766 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): -4.611000 34.22200 ymin,ymax (A): -3.399000 48.25200 zmin,zma (A): -23.60400 30.77400 x,y,z range (A): 38.83300 51.65100 54.37800 scale (grids/A): 0.6546766 object centre (A): 14.80550 22.42650 3.585000 number of atom coordinates read : 1962 total number of charged atoms : 1828 net assigned charge : 3.362005 assigned positive charge : 288.3200 centred at (gu) : 90.44446 92.55818 90.06575 assigned negative charge : -284.9583 centred at (gu) : 90.57197 92.71803 89.98433 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5760 nv = 96 ne = 84 npr = 40432 no. pairs analyzed = 40432 no. exposed pairs = 2506 no. arc points = 17229 no. surface atoms = 854 nbur = 1108 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 3191 m= 0 mr = 47 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2600000 number of dielectric boundary points 2838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1708 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6660 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2506004E-09 1.8406352E-08 midg,1,midg; midg,igrid,midg 1.6326963E-08 -2.2023549E-08 1,midg,midg; igrid,midg,midg 2.1695676E-08 -9.0692920E-09 gauss-seidel spectral radius is 0.9878497 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 11:01:31 rms-change max change #iterations 0.1312253 24.35282 at 10iterations 1.3727427E-02 2.255646 at 20iterations 1.4330343E-03 0.2176018 at 30iterations 1.4723722E-04 2.7647018E-02 at 40iterations 1.5244004E-05 2.2947788E-03 at 50iterations finished qdiffx linear iterations at : 11:01:35 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 1.5244004E-05 2.2947788E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 11:01:36 4.435u 0.404s 0:05.53 87.3% 0+0k 0+0io 6pf+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 11:01:36 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.964030 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): -4.611000 34.22200 ymin,ymax (A): -3.399000 48.25200 zmin,zma (A): -23.60400 30.77400 x,y,z range (A): 38.83300 51.65100 54.37800 scale (grids/A): 1.964030 object centre (A): 14.80550 22.42650 3.585000 number of atom coordinates read : 1962 total number of charged atoms : 1828 net assigned charge : 3.362005 assigned positive charge : 288.3200 centred at (gu) : 91.33324 97.67479 90.19753 assigned negative charge : -284.9583 centred at (gu) : 91.71615 98.15445 89.95309 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 61408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17229 grid for indexing accessible points = 1.400000 m= 22717 mr = 42406 m= 3697 mr = 17195 m= 176 mr = 2386 m= 4 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 245 time to turn everything in is 0.5300000 number of dielectric boundary points 25961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14448 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) : 0.6546766 object centre at (A) : 14.80550 22.42650 3.585000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2055894E-02 1.7650532E-02 midg,1,midg; midg,igrid,midg 4.4287723E-02 -1.6053081E-02 1,midg,midg; igrid,midg,midg 9.8687969E-03 -5.2092848E-03 gauss-seidel spectral radius is 0.9986367 estimated iterations to convergence 215 setup time was (sec) 0.8700000 now iterating at: 11:01:37 rms-change max change #iterations 3.783839 172.0303 at 10iterations 1.777081 66.07220 at 20iterations 0.8335484 30.28576 at 30iterations 0.3883461 13.14217 at 40iterations 0.1828614 6.528405 at 50iterations 8.5753918E-02 2.999152 at 60iterations 4.0071677E-02 1.468637 at 70iterations 1.8756537E-02 0.6411362 at 80iterations 8.7907268E-03 0.2928290 at 90iterations 4.1031749E-03 0.1398702 at 100iterations 1.9273672E-03 6.4590737E-02 at 110iterations 9.0040424E-04 3.0608177E-02 at 120iterations finished qdiffx linear iterations at : 11:01:47 total time elapsed so far: 10.41000 # loops : 120 mean,max change (kT/e) : 9.0040424E-04 3.0608177E-02 energy calculations done at 10.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 11:01:47 10.567u 0.470s 0:11.32 97.4% 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 Wed Dec 28 2011 at 11:01:47 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.946044 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): -4.611000 34.22200 ymin,ymax (A): -3.399000 48.25200 zmin,zma (A): -23.60400 30.77400 x,y,z range (A): 38.83300 51.65100 54.37800 scale (grids/A): 2.946044 object centre (A): 14.80550 22.42650 3.585000 number of atom coordinates read : 1962 total number of charged atoms : 1828 net assigned charge : 3.362005 assigned positive charge : 288.3200 centred at (gu) : 91.99989 101.5122 90.29619 assigned negative charge : -284.9583 centred at (gu) : 92.57425 102.2318 89.92964 start vw surface at 0.1000000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 141606 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17229 grid for indexing accessible points = 1.400000 m= 72639 mr = 102458 m= 27534 mr = 60062 m= 6733 mr = 22629 m= 911 mr = 5256 m= 40 mr = 583 m= 0 mr = 15 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 859 time to turn everything in is 1.330000 number of dielectric boundary points 58460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 14623 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) : 1.964030 object centre at (A) : 14.80550 22.42650 3.585000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9524155 6.9904588E-02 midg,1,midg; midg,igrid,midg 0.4581260 -0.2120370 1,midg,midg; igrid,midg,midg 6.5854639E-02 -2.3335757E-02 gauss-seidel spectral radius is 0.9992481 estimated iterations to convergence 288 setup time was (sec) 1.670000 now iterating at: 11:01:49 rms-change max change #iterations 8.851029 431.8685 at 10iterations 5.099329 114.6530 at 20iterations 2.926806 70.76134 at 30iterations 1.676853 32.81623 at 40iterations 0.9642643 20.11911 at 50iterations 0.5506120 12.11899 at 60iterations 0.3151816 6.094964 at 70iterations 0.1801648 3.383418 at 80iterations 0.1030117 2.130802 at 90iterations 5.8803629E-02 1.153507 at 100iterations 3.3648998E-02 0.6680355 at 110iterations 1.9190954E-02 0.3730204 at 120iterations 1.0974902E-02 0.2503548 at 130iterations 6.2788143E-03 0.1144676 at 140iterations 3.5790657E-03 6.7591667E-02 at 150iterations 2.0477418E-03 4.0026665E-02 at 160iterations 1.1683381E-03 2.2109509E-02 at 170iterations 6.6825771E-04 1.3697624E-02 at 180iterations finished qdiffx linear iterations at : 11:02:05 total time elapsed so far: 17.41000 # loops : 180 mean,max change (kT/e) : 6.6825771E-04 1.3697624E-02 energy calculations done at 17.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.58000 DelPhi exited at 11:02:08 17.587u 0.474s 0:20.55 87.8% 0+0k 0+0io 0pf+0w