------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 02/05/2008 at 17:09:30 [-O]verwriting output File Assignments: | MDIN: sander_lig.in | MDOUT: sander_lig.6.out |INPCRD: ./ciclo-enalConf20_lig.crd.6 | PARM: ligando.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: File generated by mm_pbsa.pl. Using MM GB MS &cntrl ntf = 1, ntb = 0, dielc = 1.0, idecomp= 2, igb = 2, saltcon= 0.00, offset = 0.09, intdiel= 1.0, extdiel= 80.0, gbsa = 2, surften= 1.0, cut = 999.0, nsnb = 99999, scnb = 2.0, scee = 1.2, imin = 1, maxcyc = 1, ncyc = 0, &end Residues considered as LIG LRES 2 2 END Residues to print RES 2 2 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 12/03/07 Time = 10:17:07 NATOM = 54 NTYPES = 9 NBONH = 27 MBONA = 28 NTHETH = 63 MTHETA = 37 NPHIH = 107 MPHIA = 63 NHPARM = 0 NPARM = 0 NNB = 293 NRES = 1 NBONA = 28 NTHETA = 37 NPHIA = 63 NUMBND = 14 NUMANG = 31 NPTRA = 28 NATYP = 11 NPHB = 0 IFBOX = 0 NMXRS = 54 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3950 | Hollerith 327 | Integer 27058 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 137 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- ENA General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 2, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 2, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 0.80000 gbbeta = 0.00000, gbgamma = 2.90912, surften = 1.00000 rdt = 0.00000, rgbmax = 25.00000 alpb = 0 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 LOADING THE DECOMP ATOMS AS GROUPS ----- READING GROUP 1; TITLE: Residues considered as LIG ***PROBLEMS WITH GROUPLRES 2 2 0 0 0 0 0 0 0 0 0 0 0 0******* Number of atoms in this group = 0 ----- READING GROUP 2; TITLE: Residues to print GRP 2 RES 2 TO 1 Number of atoms in this group = 0 ----- END OF GROUP READ ----- Atom 1 ( 1 ) : 0 0 Atom 2 ( 1 ) : 0 0 Atom 3 ( 1 ) : 0 0 Atom 4 ( 1 ) : 0 0 Atom 5 ( 1 ) : 0 0 Atom 6 ( 1 ) : 0 0 Atom 7 ( 1 ) : 0 0 Atom 8 ( 1 ) : 0 0 Atom 9 ( 1 ) : 0 0 Atom 10 ( 1 ) : 0 0 Atom 11 ( 1 ) : 0 0 Atom 12 ( 1 ) : 0 0 Atom 13 ( 1 ) : 0 0 Atom 14 ( 1 ) : 0 0 Atom 15 ( 1 ) : 0 0 Atom 16 ( 1 ) : 0 0 Atom 17 ( 1 ) : 0 0 Atom 18 ( 1 ) : 0 0 Atom 19 ( 1 ) : 0 0 Atom 20 ( 1 ) : 0 0 Atom 21 ( 1 ) : 0 0 Atom 22 ( 1 ) : 0 0 Atom 23 ( 1 ) : 0 0 Atom 24 ( 1 ) : 0 0 Atom 25 ( 1 ) : 0 0 Atom 26 ( 1 ) : 0 0 Atom 27 ( 1 ) : 0 0 Atom 28 ( 1 ) : 0 0 Atom 29 ( 1 ) : 0 0 Atom 30 ( 1 ) : 0 0 Atom 31 ( 1 ) : 0 0 Atom 32 ( 1 ) : 0 0 Atom 33 ( 1 ) : 0 0 Atom 34 ( 1 ) : 0 0 Atom 35 ( 1 ) : 0 0 Atom 36 ( 1 ) : 0 0 Atom 37 ( 1 ) : 0 0 Atom 38 ( 1 ) : 0 0 Atom 39 ( 1 ) : 0 0 Atom 40 ( 1 ) : 0 0 Atom 41 ( 1 ) : 0 0 Atom 42 ( 1 ) : 0 0 Atom 43 ( 1 ) : 0 0 Atom 44 ( 1 ) : 0 0 Atom 45 ( 1 ) : 0 0 Atom 46 ( 1 ) : 0 0 Atom 47 ( 1 ) : 0 0 Atom 48 ( 1 ) : 0 0 Atom 49 ( 1 ) : 0 0 Atom 50 ( 1 ) : 0 0 Atom 51 ( 1 ) : 0 0 Atom 52 ( 1 ) : 0 0 Atom 53 ( 1 ) : 0 0 Atom 54 ( 1 ) : 0 0 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- trajectory generated by ptraj begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 7.5658E+02 1.5785E+01 4.9289E+01 C12 19 BOND = 14.1010 ANGLE = 31.0835 DIHED = 22.9947 VDWAALS = -8.5891 EEL = -264.8472 EGB = -99.6474 1-4 VDW = 12.3136 1-4 EEL = 389.7498 RESTRAINT = 0.0000 ESURF = 659.4184 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 7.5658E+02 1.5785E+01 4.9289E+01 C12 19 BOND = 14.1010 ANGLE = 31.0835 DIHED = 22.9947 VDWAALS = -8.5891 EEL = -264.8472 EGB = -99.6474 1-4 VDW = 12.3136 1-4 EEL = 389.7498 RESTRAINT = 0.0000 ESURF = 659.4184 CHECK DECOMP - TOTAL ENERGIES (w/ REST) INTERNAL= 68.1792 VDWAALS = 3.7245 EEL = 124.9026 EGB = -99.6474 ESURF = 659.4184 CHECK DECOMP - SELF ENERGIES (w/o REST) INTERNAL= 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EGB = 0.0000 ESURF = 0.0000 CHECK DECOMP - INDIRECT ENERGIES (w/o REST) INTERNAL= 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EGB = 0.0000 ESURF = 0.0000 CHECK DECOMP - DIRECT ENERGIES (w/o REST) INTERNAL= 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EGB = 0.0000 ESURF = 0.0000 CHECK DECOMP - REST ENERGIES INTERNAL= 68.1792 VDWAALS = 3.7245 EEL = 124.9026 EGB = -99.6474 ESURF = 659.4184 PRINT DECOMP - TOTAL ENERGIES resid |internal |vdw |eel |pol |sas ============================================================ PRINT DECOMP - SIDECHAIN ENERGIES resid |internal |vdw |eel |pol |sas ============================================================ PRINT DECOMP - BACKBONE ENERGIES resid |internal |vdw |eel |pol |sas ============================================================ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 0.39% of Total) | Fast Water setup 0.00 ( 0.02% of Total) | Calc gb radii 0.00 ( 0.40% of Gen B) | Calc gb diag 0.12 (98.82% of Gen B) | Calc gb off-diag 0.00 ( 0.76% of Gen B) | Other 0.00 ( 0.02% of Gen B) | Gen Born time 0.13 (100.0% of Nonbo) | Nonbond force 0.13 (99.65% of Force) | Bond/Angle/Dihedral 0.00 ( 0.33% of Force) | Other 0.00 ( 0.02% of Force) | Force time 0.13 (100.0% of Runmd) | Runmd Time 0.13 (93.21% of Total) | Other 0.01 ( 6.38% of Total) | Total time 0.14 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 17:09:30.385 on 02/05/2008 | Setup done at 17:09:30.393 on 02/05/2008 | Run done at 17:09:30.521 on 02/05/2008 | wallclock() was called 26 times