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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Thu, Sep 18, 2014 at 11:26 AM, Asfa Ali <asfa.iisc.gmail.com> wrote: > Yes, the message in pbsa_lig.77.out also indicates about fillratio. > How to go about this and where exactly should I include the fillratio? > > Here is the out file: > > pbsa_lig.77.out > > ------------------------------------------------------- > Amber 9 PBSA Scripps/UCSF 2006 > ------------------------------------------------------- > > | Run on 09/18/2014 at 19:20:32 > [-O]verwriting output > > File Assignments: > | MDIN: pbsa.in > > | MDOUT: > pbsa_lig.77.out > |INPCRD: > ./snapshot_lig.crd.77 > | PARM: > ./lig_vac.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 > PB > &cntrl > > ntf = 1, ntb = > 0, > igb = 10, dielc = > 1.0, > cut = 999.0, nsnb = > 99999, > scnb = 2.0, scee = > 1.2, > imin = 1, maxcyc = 0, ntmin = > 2, > &end > > &pb > > epsin = 1.0, epsout = > 80.0, > istrng = 0, radiopt = > 0, > sprob = 1.4, space = > 0.5, > maxitn = 1000, npopt = > 1, > cavity_surften = 0.0072, cavity_offset = > 0.00, > npbverb= > 1 > &end > > > -------------------------------------------------------------------------------- > 1. RESOURCE USE: > -------------------------------------------------------------------------------- > > | > Flags: > > | New format PARM file being parsed. > | Version = 1.000 Date = 05/25/10 Time = 12:37:34 > NATOM = 90 NTYPES = 7 NBONH = 38 MBONA = 60 > NTHETH = 76 MTHETA = 88 NPHIH = 142 MPHIA = 144 > NHPARM = 0 NPARM = 0 NNB = 486 NRES = 1 > NBONA = 60 NTHETA = 88 NPHIA = 144 NUMBND = 19 > NUMANG = 36 NPTRA = 9 NATYP = 11 NPHB = 0 > IFBOX = 0 NMXRS = 90 IFCAP = 0 NEXTRA = 0 > NCOPY = 0 > > > | Memory Use Allocated > | Real 3395 > | Hollerith 543 > | Integer 24315 > | Max Pairs 1 > | Max Rstack 1 > | Max Istack 1 > | Total 123 kbytes > | Duplicated 0 dihedrals > | Duplicated 0 dihedrals > > -------------------------------------------------------------------------------- > 2. CONTROL DATA FOR THE RUN > -------------------------------------------------------------------------------- > > LIG > > > 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 = 0, > rbornstat= 0 > > Potential function: > ntf = 1, ntb = 0, igb = 10, nsnb = > 99999 > ipol = 0, gbsa = 0, iesp = 0 > dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 > scnb = 2.00000, scee = 1.20000 > > Frozen or restrained atoms: > ibelly = 0, ntr = 0 > > Energy minimization: > maxcyc = 0, ncyc = 10, ntmin = 2 > dx0 = 0.01000, drms = 0.00010 > > ======== Implicit Solvent Initialization ======== > > Max Nonbonded Pairs: 4051 4051 4051 > > no. of atoms processed in PB initialization: 90 > NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI > 1 LIG C cc -0.123000 0.044000 0.045000 1.700000 1.700000 > 2 LIG C1 cd -0.257600 -0.091600 0.468300 1.700000 1.700000 > 3 LIG C2 cd 0.515900 0.515900 -0.394800 1.700000 1.700000 > 4 LIG N nc -0.619300 -0.619300 -0.010800 1.550000 1.550000 > 5 LIG C3 cf 0.081600 0.081600 0.135300 1.700000 1.700000 > 6 LIG C4 cc 0.092600 0.092600 -0.401100 1.700000 1.700000 > 7 LIG C5 cd -0.086100 -0.086100 0.268100 1.700000 1.700000 > 8 LIG C6 cc -0.146000 0.019000 -0.048100 1.700000 1.700000 > 9 LIG N1 na -0.089100 0.253600 0.081400 1.550000 1.550000 > 10 LIG C7 cc -0.146000 0.019000 -0.048100 1.700000 1.700000 > 11 LIG C8 cd -0.086100 -0.086100 0.268100 1.700000 1.700000 > 12 LIG H hn 0.342700 0.342700 0.342700 1.300000 1.300000 > 13 LIG C9 cf 0.081600 0.081600 0.135300 1.700000 1.700000 > 14 LIG C10 cc 0.092600 0.092600 -0.401100 1.700000 1.700000 > 15 LIG C11 cc -0.123000 0.044000 0.045000 1.700000 1.700000 > 16 LIG N2 nc -0.619300 -0.619300 -0.010800 1.550000 1.550000 > 17 LIG C12 cd -0.257600 -0.091600 0.468300 1.700000 1.700000 > 18 LIG C13 cd 0.515900 0.515900 -0.394800 1.700000 1.700000 > 19 LIG C14 cf -0.199800 -0.199800 0.508000 1.700000 1.700000 > 20 LIG C15 cd 0.098900 0.098900 0.081700 1.700000 1.700000 > 21 LIG C16 cc -0.123000 0.058000 0.214900 1.700000 1.700000 > 22 LIG N3 na -0.229100 0.124600 0.322400 1.550000 1.550000 > 23 LIG C17 cc -0.123000 0.058000 0.214900 1.700000 1.700000 > 24 LIG C18 cd 0.098900 0.098900 0.081700 1.700000 1.700000 > 25 LIG H1 hn 0.353700 0.353700 0.353700 1.300000 1.300000 > 26 LIG C19 cf -0.199800 -0.199800 0.508000 1.700000 1.700000 > 27 LIG C20 ca 0.047200 0.047200 0.277800 1.700000 1.700000 > 28 LIG C21 ca -0.131000 0.075000 0.324900 1.700000 1.700000 > 29 LIG C22 ca -0.023300 0.202700 0.325600 1.700000 1.700000 > 30 LIG N4 na 0.047900 0.047900 0.755000 1.550000 1.550000 > 31 LIG C23 ca -0.023300 0.201700 0.323600 1.700000 1.700000 > 32 LIG C24 c3 -0.042400 0.302700 0.350600 1.700000 1.700000 > 33 LIG C25 ca -0.132000 0.074000 0.322900 1.700000 1.700000 > 34 LIG C26 cc 0.093000 0.093000 0.000200 1.700000 1.700000 > 35 LIG C27 cc -0.143000 0.059000 0.459000 1.700000 1.700000 > 36 LIG C28 cd 0.084000 0.307000 0.018800 1.700000 1.700000 > 37 LIG N5 na -0.347200 -0.347200 0.748000 1.550000 1.550000 > 38 LIG C29 cd 0.087000 0.310000 0.010800 1.700000 1.700000 > 39 LIG C30 c3 0.137100 0.478200 0.131000 1.700000 1.700000 > 40 LIG C31 cc -0.151000 0.048000 0.451000 1.700000 1.700000 > 41 LIG C32 ca 0.047200 0.047200 0.277800 1.700000 1.700000 > 42 LIG C33 ca -0.131000 0.075000 0.324900 1.700000 1.700000 > 43 LIG C34 ca -0.023300 0.202700 0.325600 1.700000 1.700000 > 44 LIG N6 na 0.047900 0.047900 0.755000 1.550000 1.550000 > 45 LIG C35 ca -0.023300 0.201700 0.323600 1.700000 1.700000 > 46 LIG C36 c3 -0.042400 0.302700 0.350600 1.700000 1.700000 > 47 LIG C37 ca -0.132000 0.074000 0.322900 1.700000 1.700000 > 48 LIG C38 cc 0.093000 0.093000 0.000200 1.700000 1.700000 > 49 LIG C39 cc -0.151000 0.048000 0.451000 1.700000 1.700000 > 50 LIG C40 cd 0.087000 0.310000 0.010800 1.700000 1.700000 > 51 LIG N7 na -0.347200 -0.347200 0.748000 1.550000 1.550000 > 52 LIG C41 cd 0.084000 0.307000 0.018800 1.700000 1.700000 > 53 LIG C42 c3 0.137100 0.478200 0.131000 1.700000 1.700000 > 54 LIG C43 cc -0.143000 0.059000 0.459000 1.700000 1.700000 > 55 LIG H2 ha 0.167000 0.167000 0.167000 1.300000 1.300000 > 56 LIG H3 ha 0.166000 0.166000 0.166000 1.300000 1.300000 > 57 LIG H4 ha 0.165000 0.165000 0.165000 1.300000 1.300000 > 58 LIG H5 ha 0.165000 0.165000 0.165000 1.300000 1.300000 > 59 LIG H6 ha 0.167000 0.167000 0.167000 1.300000 1.300000 > 60 LIG H7 ha 0.166000 0.166000 0.166000 1.300000 1.300000 > 61 LIG H8 ha 0.181000 0.181000 0.181000 1.300000 1.300000 > 62 LIG H9 ha 0.181000 0.181000 0.181000 1.300000 1.300000 > 63 LIG H10 ha 0.206000 0.206000 0.206000 1.300000 1.300000 > 64 LIG H11 h4 0.226000 0.226000 0.226000 1.300000 1.300000 > 65 LIG H12 h4 0.225000 0.225000 0.225000 1.300000 1.300000 > 66 LIG H13 h1 0.114700 0.114700 0.114700 1.300000 1.300000 > 67 LIG H14 h1 0.115700 0.115700 0.115700 1.300000 1.300000 > 68 LIG H15 h1 0.114700 0.114700 0.114700 1.300000 1.300000 > 69 LIG H16 ha 0.206000 0.206000 0.206000 1.300000 1.300000 > 70 LIG H17 ha 0.202000 0.202000 0.202000 1.300000 1.300000 > 71 LIG H18 h4 0.223000 0.223000 0.223000 1.300000 1.300000 > 72 LIG H19 h4 0.223000 0.223000 0.223000 1.300000 1.300000 > 73 LIG H20 h1 0.113700 0.113700 0.113700 1.300000 1.300000 > 74 LIG H21 h1 0.114700 0.114700 0.114700 1.300000 1.300000 > 75 LIG H22 h1 0.112700 0.112700 0.112700 1.300000 1.300000 > 76 LIG H23 ha 0.199000 0.199000 0.199000 1.300000 1.300000 > 77 LIG H24 ha 0.206000 0.206000 0.206000 1.300000 1.300000 > 78 LIG H25 h4 0.226000 0.226000 0.226000 1.300000 1.300000 > 79 LIG H26 h4 0.225000 0.225000 0.225000 1.300000 1.300000 > 80 LIG H27 h1 0.114700 0.114700 0.114700 1.300000 1.300000 > 81 LIG H28 h1 0.115700 0.115700 0.115700 1.300000 1.300000 > 82 LIG H29 h1 0.114700 0.114700 0.114700 1.300000 1.300000 > 83 LIG H30 ha 0.206000 0.206000 0.206000 1.300000 1.300000 > 84 LIG H31 ha 0.199000 0.199000 0.199000 1.300000 1.300000 > 85 LIG H32 h4 0.223000 0.223000 0.223000 1.300000 1.300000 > 86 LIG H33 h4 0.223000 0.223000 0.223000 1.300000 1.300000 > 87 LIG H34 h1 0.113700 0.113700 0.113700 1.300000 1.300000 > 88 LIG H35 h1 0.114700 0.114700 0.114700 1.300000 1.300000 > 89 LIG H36 h1 0.112700 0.112700 0.112700 1.300000 1.300000 > 90 LIG H37 ha 0.202000 0.202000 0.202000 1.300000 1.300000 > > total system charges (+/-) for PB 4.0030 9.4172 -5.4142 > cavity_surften = 0.0072 cavity_offset = 0.0000 > > SAS Surface: surface dots generated: 366 > > -------------------------------------------------------------------------------- > 3. ATOMIC COORDINATES AND VELOCITIES > -------------------------------------------------------------------------------- > > > > begin time read from input coords = 0.000 ps > > Number of triangulated 3-point waters found: 0 > > -------------------------------------------------------------------------------- > 4. RESULTS > -------------------------------------------------------------------------------- > > NB-update: residue-based nb list 3535 > NB-update: atom-based nb list 2292 > > > ======== Setting up Grid Parameters ======== > Using bounding box for grid setup > Bounding Box Center: 64.000 43.000 18.000 > Xmin, Xmax, Xmax-Xmin: 59.729 68.710 8.981 > Ymin, Ymax, Ymax-Ymin: 32.255 53.504 21.249 > Zmin, Zmax, Zmax-Zmin: 7.106 28.945 21.839 > beginning box center at level 1 64.000 43.000 18.000 > beginning box center at level 2 64.000 43.000 18.000 > Grid dimension at level 1 5 13 13 > Grid origin corrected at level 1 52.000 15.000 -10.000 > Grid dimension at level 2 33 57 59 > Grid origin corrected at level 2 55.500 28.500 3.000 > PB Bomb in setgrd(): focusing grid too large 2 > reset fillratio to a larger number 2.000 > > On Thu, Sep 18, 2014 at 8:12 PM, Jason Swails <jason.swails.gmail.com> > wrote: > >> On Thu, 2014-09-18 at 19:40 +0530, Asfa Ali wrote: >> > Hi, >> > >> > While running mm_pbsa.pl of a ligand-dna complex, I got the following >> error >> > message: >> > >> > /data/software/amber91/exe/pbsa -O -i pbsa.in -o pbsa_lig.77.out -c >> > ./snapshot_lig.crd.77 -p ./lig_vac.prmtop not successful >> > >> > The snapshot_com.all.out and snapshot_rec.all.out are fine, only in the >> > case of lig, it is stopping at 77. >> > >> > I checked the ambermailing list and added the line "fillratio = 4.0" in >> the >> > pbsa.in file generated but still the error persists. >> >> Look for the error message inside pbsa_lig.77.out. Try using that error >> message as a starting point for an online search. >> >> HTH, >> Jason >> >> -- >> Jason M. Swails >> BioMaPS, >> Rutgers University >> Postdoctoral Researcher >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > > > -- > Asfa Ali > Prof. S. Bhattacharya's group, > Dept. of Organic Chemistry, > Indian Institute of Science, > Bangalore-12 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Sep 18 2014 - 12:00:03 PDT