Re: [AMBER] MMPBSA

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Thu, 18 Sep 2014 11:32:32 -0700

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