Mon Oct 10 22:34:36 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 Mon Oct 10 2011 at 22:34:36 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2625 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 0.6178839 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): 17.62600 75.24200 ymin,ymax (A): -11.14900 43.18200 zmin,zma (A): -8.477000 34.94900 x,y,z range (A): 57.61600 54.33100 43.42600 scale (grids/A): 0.6178839 object centre (A): 46.43400 16.01650 13.23600 number of atom coordinates read : 2625 total number of charged atoms : 2480 net assigned charge : 5.406018 assigned positive charge : 394.3078 centred at (gu) : 88.41656 89.99325 89.95667 assigned negative charge : -388.9025 centred at (gu) : 88.71217 90.11417 90.13773 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6563 nv = 96 ne = 84 npr = 53738 no. pairs analyzed = 53738 no. exposed pairs = 3023 no. arc points = 21085 no. surface atoms = 1026 nbur = 1599 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 288 mr = 3723 m= 0 mr = 31 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.2900000 number of dielectric boundary points 3097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2085 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8083 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5021305E-08 -7.7000228E-09 midg,1,midg; midg,igrid,midg 1.1259101E-08 -3.8803845E-09 1,midg,midg; igrid,midg,midg 3.0941610E-08 -1.0712109E-08 gauss-seidel spectral radius is 0.9864331 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 22:34:37 rms-change max change #iterations 0.1269535 17.83228 at 10iterations 1.2148147E-02 1.929177 at 20iterations 1.6525190E-03 0.3097305 at 30iterations 3.9109049E-04 9.1064453E-02 at 40iterations 1.1341397E-04 2.7336121E-02 at 50iterations finished qdiffx linear iterations at : 22:34:40 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 1.1341397E-04 2.7336121E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 22:34:40 3.297u 0.191s 0:04.01 86.7% 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 Mon Oct 10 2011 at 22:34:40 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2625 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 1.853652 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): 17.62600 75.24200 ymin,ymax (A): -11.14900 43.18200 zmin,zma (A): -8.477000 34.94900 x,y,z range (A): 57.61600 54.33100 43.42600 scale (grids/A): 1.853652 object centre (A): 46.43400 16.01650 13.23600 number of atom coordinates read : 2625 total number of charged atoms : 2480 net assigned charge : 5.406018 assigned positive charge : 394.3078 centred at (gu) : 85.24907 89.97921 89.86954 assigned negative charge : -388.9025 centred at (gu) : 86.13651 90.34211 90.41309 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21085 grid for indexing accessible points = 1.400000 m= 24688 mr = 50760 m= 3534 mr = 18517 m= 150 mr = 2254 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2818 time to turn everything in is 0.4900000 number of dielectric boundary points 28472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19422 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) : 0.6178839 object centre at (A) : 46.43400 16.01650 13.23600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9246278E-02 1.0269649E-03 midg,1,midg; midg,igrid,midg 3.5687767E-02 7.8424141E-03 1,midg,midg; igrid,midg,midg 4.4188602E-03 -5.5363663E-02 gauss-seidel spectral radius is 0.9985568 estimated iterations to convergence 209 setup time was (sec) 0.7600000 now iterating at: 22:34:41 rms-change max change #iterations 4.047504 154.9802 at 10iterations 1.845030 66.93298 at 20iterations 0.8450623 27.35136 at 30iterations 0.3875251 13.92412 at 40iterations 0.1782955 5.513990 at 50iterations 8.1932865E-02 2.613215 at 60iterations 3.7759863E-02 1.217140 at 70iterations 1.7394109E-02 0.5823591 at 80iterations 8.1418063E-03 0.2628937 at 90iterations 3.9081289E-03 0.1478577 at 100iterations 1.9204656E-03 7.2177887E-02 at 110iterations 1.0091949E-03 4.1509628E-02 at 120iterations finished qdiffx linear iterations at : 22:34:48 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 1.0091949E-03 4.1509628E-02 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 22:34:49 7.355u 0.208s 0:08.24 91.6% 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 Mon Oct 10 2011 at 22:34:49 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2625 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 2.780478 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): 17.62600 75.24200 ymin,ymax (A): -11.14900 43.18200 zmin,zma (A): -8.477000 34.94900 x,y,z range (A): 57.61600 54.33100 43.42600 scale (grids/A): 2.780478 object centre (A): 46.43400 16.01650 13.23600 number of atom coordinates read : 2625 total number of charged atoms : 2480 net assigned charge : 5.406018 assigned positive charge : 394.3078 centred at (gu) : 82.87347 89.96874 89.80415 assigned negative charge : -388.9025 centred at (gu) : 84.20467 90.51309 90.61955 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 166246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21085 grid for indexing accessible points = 1.400000 m= 82042 mr = 122845 m= 28000 mr = 67995 m= 6372 mr = 22923 m= 738 mr = 4929 m= 17 mr = 487 m= 0 mr = 4 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 9678 time to turn everything in is 1.220000 number of dielectric boundary points 64232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 19840 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) : 1.853652 object centre at (A) : 46.43400 16.01650 13.23600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2946827 4.0340498E-02 midg,1,midg; midg,igrid,midg 0.4169151 0.1475885 1,midg,midg; igrid,midg,midg -0.1007465 -0.7243478 gauss-seidel spectral radius is 0.9992338 estimated iterations to convergence 285 setup time was (sec) 1.520000 now iterating at: 22:34:50 rms-change max change #iterations 9.522539 384.9247 at 10iterations 5.458677 114.1070 at 20iterations 3.117513 76.88010 at 30iterations 1.775346 36.03934 at 40iterations 1.012330 19.99634 at 50iterations 0.5771845 10.50946 at 60iterations 0.3286193 6.477947 at 70iterations 0.1867943 3.594177 at 80iterations 0.1064532 2.049316 at 90iterations 6.0593616E-02 1.169559 at 100iterations 3.4450948E-02 0.6399832 at 110iterations 1.9668236E-02 0.3919678 at 120iterations 1.1276990E-02 0.2194977 at 130iterations 6.5246001E-03 0.1459503 at 140iterations 3.8002932E-03 8.0907822E-02 at 150iterations 2.2731861E-03 5.4428101E-02 at 160iterations 1.4073844E-03 3.3039093E-02 at 170iterations 9.1890479E-04 2.3155212E-02 at 180iterations finished qdiffx linear iterations at : 22:35:00 total time elapsed so far: 11.60000 # loops : 180 mean,max change (kT/e) : 9.1890479E-04 2.3155212E-02 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 22:35:01 11.788u 0.251s 0:12.41 96.9% 0+0k 0+0io 0pf+0w