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
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Received on Thu Sep 18 2014 - 12:00:03 PDT
