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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 11:39 AM, Asfa Ali <asfa.iisc.gmail.com> wrote: > No Sir, it is Amber 9. > > On Fri, Sep 19, 2014 at 12:02 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote: > >> Is this from using Amber14? >> >> Ray >> -- >> 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/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 - 12:00:04 PDT