Tue Oct 11 03:36:03 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 Tue Oct 11 2011 at 03:36:03 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 !!! WARNING: ASL 116 has a net charge of -0.1000 !!! WARNING: HIR 220 has a net charge of 0.5140 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: 0.6039733 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): 12.84500 61.04900 ymin,ymax (A): -30.95100 27.99200 zmin,zma (A): 3.101000 60.54500 x,y,z range (A): 48.20400 58.94300 57.44400 scale (grids/A): 0.6039733 object centre (A): 36.94700 -1.479500 31.82300 number of atom coordinates read : 2498 total number of charged atoms : 2418 net assigned charge : -8.5985690E-02 assigned positive charge : 380.0088 centred at (gu) : 92.33243 89.79485 89.94565 assigned negative charge : -380.0954 centred at (gu) : 92.32161 90.05770 89.92553 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6212 nv = 96 ne = 84 npr = 48247 no. pairs analyzed = 48247 no. exposed pairs = 3478 no. arc points = 24943 no. surface atoms = 1155 nbur = 1343 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 3057 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2900000 number of dielectric boundary points 3462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2415 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7657 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8170599E-10 7.3498974E-10 midg,1,midg; midg,igrid,midg 1.0668821E-08 -1.0434110E-08 1,midg,midg; igrid,midg,midg -2.9307740E-10 6.4352351E-10 gauss-seidel spectral radius is 0.9858133 estimated iterations to convergence 69 setup time was (sec) 0.5300000 now iterating at: 03:36:04 rms-change max change #iterations 0.1083602 16.75883 at 10iterations 9.3851797E-03 1.439407 at 20iterations 8.0363598E-04 0.1154785 at 30iterations 7.0970185E-05 1.1898756E-02 at 40iterations 6.6004150E-06 9.2792511E-04 at 50iterations finished qdiffx linear iterations at : 03:36:07 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 6.6004150E-06 9.2792511E-04 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 03:36:08 3.331u 0.213s 0:04.50 78.6% 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 Tue Oct 11 2011 at 03:36:08 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 !!! WARNING: ASL 116 has a net charge of -0.1000 !!! WARNING: HIR 220 has a net charge of 0.5140 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: 1.811920 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): 12.84500 61.04900 ymin,ymax (A): -30.95100 27.99200 zmin,zma (A): 3.101000 60.54500 x,y,z range (A): 48.20400 58.94300 57.44400 scale (grids/A): 1.811920 object centre (A): 36.94700 -1.479500 31.82300 number of atom coordinates read : 2498 total number of charged atoms : 2418 net assigned charge : -8.5985690E-02 assigned positive charge : 380.0088 centred at (gu) : 96.99677 89.38390 89.83656 assigned negative charge : -380.0954 centred at (gu) : 96.96477 90.17260 89.77621 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 66851 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24943 grid for indexing accessible points = 1.400000 m= 22152 mr = 43465 m= 3037 mr = 15111 m= 119 mr = 1659 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 412 time to turn everything in is 0.5100000 number of dielectric boundary points 31904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 18888 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) : 0.6039733 object centre at (A) : 36.94700 -1.479500 31.82300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0705577E-02 3.7606603E-03 midg,1,midg; midg,igrid,midg 3.7005544E-02 -4.7963247E-02 1,midg,midg; igrid,midg,midg 5.8999551E-03 2.2797817E-02 gauss-seidel spectral radius is 0.9985014 estimated iterations to convergence 205 setup time was (sec) 0.8000000 now iterating at: 03:36:09 rms-change max change #iterations 3.769618 176.6673 at 10iterations 1.696989 72.82470 at 20iterations 0.7656154 29.22308 at 30iterations 0.3454344 11.75427 at 40iterations 0.1552751 5.083504 at 50iterations 6.9975667E-02 2.333557 at 60iterations 3.1501520E-02 1.099487 at 70iterations 1.4208159E-02 0.4976187 at 80iterations 6.4264019E-03 0.2156601 at 90iterations 2.8964397E-03 0.1042023 at 100iterations 1.3077633E-03 4.4767380E-02 at 110iterations 5.8945623E-04 1.9998550E-02 at 120iterations finished qdiffx linear iterations at : 03:36:15 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 5.8945623E-04 1.9998550E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 03:36:16 7.509u 0.213s 0:08.05 95.7% 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 Tue Oct 11 2011 at 03:36:16 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 !!! WARNING: ASL 116 has a net charge of -0.1000 !!! WARNING: HIR 220 has a net charge of 0.5140 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: 2.717880 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): 12.84500 61.04900 ymin,ymax (A): -30.95100 27.99200 zmin,zma (A): 3.101000 60.54500 x,y,z range (A): 48.20400 58.94300 57.44400 scale (grids/A): 2.717880 object centre (A): 36.94700 -1.479500 31.82300 number of atom coordinates read : 2498 total number of charged atoms : 2418 net assigned charge : -8.5985690E-02 assigned positive charge : 380.0088 centred at (gu) : 100.4950 89.07564 89.75481 assigned negative charge : -380.0954 centred at (gu) : 100.4471 90.25877 89.66433 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 154998 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24943 grid for indexing accessible points = 1.400000 m= 71992 mr = 106528 m= 24627 mr = 56167 m= 5136 mr = 18746 m= 510 mr = 3470 m= 24 mr = 296 m= 0 mr = 6 time to grow re-entrant surface = 0.6600001 no. cavity mid-points inaccessible to solvent = 1302 time to turn everything in is 1.210000 number of dielectric boundary points 72074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 19341 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) : 1.811920 object centre at (A) : 36.94700 -1.479500 31.82300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3639164 0.5808191 midg,1,midg; midg,igrid,midg 0.5612059 -0.5324636 1,midg,midg; igrid,midg,midg 6.7009985E-02 0.2767088 gauss-seidel spectral radius is 0.9992322 estimated iterations to convergence 285 setup time was (sec) 1.520000 now iterating at: 03:36:18 rms-change max change #iterations 9.312819 265.4570 at 10iterations 5.430452 134.4177 at 20iterations 3.143915 75.37656 at 30iterations 1.817001 44.35250 at 40iterations 1.039803 23.84138 at 50iterations 0.5956928 13.28691 at 60iterations 0.3410902 8.071990 at 70iterations 0.1944633 4.096046 at 80iterations 0.1109872 2.305384 at 90iterations 6.3099749E-02 1.449924 at 100iterations 3.5898607E-02 0.7826371 at 110iterations 2.0436088E-02 0.4097719 at 120iterations 1.1628111E-02 0.2332282 at 130iterations 6.6044205E-03 0.1389313 at 140iterations 3.7516297E-03 7.6660156E-02 at 150iterations 2.1316162E-03 4.2823792E-02 at 160iterations 1.2110283E-03 2.4255753E-02 at 170iterations 6.8697822E-04 1.4316559E-02 at 180iterations finished qdiffx linear iterations at : 03:36:28 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 6.8697822E-04 1.4316559E-02 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 03:36:29 12.199u 0.235s 0:12.72 97.6% 0+0k 0+0io 0pf+0w