AMBER Archive (2009)

Subject: Re: [AMBER] MM_PBSA not successful

From: workalemahu berhanu (wgberhanu_at_gmail.com)
Date: Fri Aug 14 2009 - 21:21:32 CDT

Dear Jorden

hi

Please find the content of fine pbsa_com.1.out . Thank you
 -------------------------------------------------------
          Amber 9 PBSA Scripps/UCSF 2006
          -------------------------------------------------------

| Run on 08/14/2009 at 19:13:47
  [-O]verwriting output

File Assignments:
| MDIN: pbsa.in
| MDOUT: pbsa_com.1.out
|INPCRD: ./snapshot_com.crd.1
| PARM: ./GNNQQNYMYRSB.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 = 07/27/09 Time = 17:43:38
 NATOM = 1103 NTYPES = 12 NBONH = 490 MBONA = 615
 NTHETH = 1064 MTHETA = 828 NPHIH = 2382 MPHIA = 1873
 NHPARM = 0 NPARM = 0 NNB = 5759 NRES = 71
 NBONA = 615 NTHETA = 828 NPHIA = 1873 NUMBND = 30
 NUMANG = 53 NPTRA = 29 NATYP = 23 NPHB = 0
 IFBOX = 0 NMXRS = 33 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 40858
| Hollerith 6691
| Integer 74998
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 638 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

General flags:
     imin = 1, nmropt = 0
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: 608305 268029 608305

  no. of atoms processed in PB initialization: 1103
  NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI
    1 GLY N N3 0.294300 0.786900 0.955900 1.550000 1.550000
    2 GLY H1 H 0.164200 0.000000 0.000000 1.300000 1.300000
    3 GLY H2 H 0.164200 0.000000 0.000000 1.300000 1.300000
    4 GLY H3 H 0.164200 0.000000 0.000000 1.300000 1.300000
    5 GLY CA CT -0.010000 0.169000 1.572200 1.700000 1.700000
    6 GLY HA2 HP 0.089500 0.000000 0.000000 1.200000 1.200000
    7 GLY HA3 HP 0.089500 0.000000 0.000000 1.200000 1.200000
    8 GLY C C 0.616300 0.616300 0.069300 1.700000 1.700000
    9 GLY O O -0.572200 -0.572200 0.044100 1.500000 1.500000
   10 ASN N N -0.415700 -0.143800 0.591600 1.550000 1.550000
   11 ASN H H 0.271900 0.000000 0.000000 1.300000 1.300000
   12 ASN CA CT 0.014300 0.119100 0.527900 1.700000 1.700000
------------------------------------------------------------------------------------------------------
1103 MOL H28 ho 0.425230 0.425230 0.425230 1.200000 1.200000

 total system charges (+/-) for PB 0.0000 180.9628 -180.9628
 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

On Fri, Aug 14, 2009 at 8:05 PM, Jordan Monnet<monnet.jordan_at_free.fr> wrote:
> Hello,
>
> What does pbsa_com.1.out say?
>
> --jordan
>
> * workalemahu berhanu (wgberhanu_at_gmail.com) wrote:
>> Dear Amber users
>>
>> I am not getting the results for mmpbsa calculation Calculate the
>> binding free energy. Can anyone help me?
>> I have
>> given both my input and output files.
>> This is my input
>> @GENERAL
>> PREFIX                snapshot
>> PATH                  ./
>> COMPLEX               1
>> RECEPTOR              1
>> LIGAND                1
>> COMPT                 ./GNNQQNYMYRSB.prmtop
>> RECPT                 ./GNNQQNYSB.prmtop
>> LIGPT                 ./MYR.prmtop
>> GC                    0
>> AS                    0
>> DC                    0
>> MM                    1
>> GB                    2
>> PB                    1
>> MS                    1
>> NM                    0
>> @PB
>> PROC                  2
>> REFE                  0
>> INDI                  1.0
>> EXDI                  80.0
>> SCALE                 2
>> LINIT                 1000
>> PRBRAD                1.4
>> ISTRNG                0.0
>> RADIOPT               0
>> NPOPT                 1
>> CAVITY_SURFTEN        0.0072
>> CAVITY_OFFSET         0.00
>> SURFTEN               0.0072
>> SURFOFF               0.00
>> @MM
>> DIELC                 1.0
>> @GB
>> IGB                   2
>> GBSA                  1
>> SALTCON               0.00
>> EXTDIEL               80.0
>> INTDIEL               1.0
>> SURFTEN              0.0072
>> SURFOFF              0.00
>> @MS
>> PROBE                 0.0
>> @PROGRAMS
>>  This is my Out put
>> =>> Init data
>>     Presuming executables of amber suite to be in /u0/z/zz217/USG/amber/9.0/exe
>>
>> =>> Reading input parameters
>>     Found PREFIX => snapshot
>>     Found PATH => ./
>>     Found COMPLEX => 1
>>     Found RECEPTOR => 1
>>     Found LIGAND => 1
>>     Found COMPT => ./GNNQQNYMYRSB.prmtop
>>     Found RECPT => ./GNNQQNYSB.prmtop
>>     Found LIGPT => ./MYR.prmtop
>>     Found GC => 0
>>     Found AS => 0
>>     Found DC => 0
>>     Found MM => 1
>>     Found GB => 2
>>     Found PB => 1
>>     Found MS => 1
>>     Found NM => 0
>>     Found PROC => 2
>>     Found REFE => 0
>>     Found INDI => 1.0
>>     Found EXDI => 80.0
>>     Found SCALE => 2
>>     Found LINIT => 1000
>>     Found PRBRAD => 1.4
>>     Found ISTRNG => 0.0
>>     Found RADIOPT => 0
>>     Found NPOPT => 1
>>     Found CAVITY_SURFTEN => 0.0072
>>     Found CAVITY_OFFSET => 0.00
>>     Found SURFTEN => 0.0072
>>     Found SURFOFF => 0.00
>>     Found DIELC => 1.0
>>     Found IGB => 2
>>     Found GBSA => 1
>>     Found SALTCON => 0.00
>>     Found EXTDIEL => 80.0
>>     Found INTDIEL => 1.0
>>     Found SURFTEN => 0.0072
>>     Found SURFOFF => 0.00
>> Found PROBE => 0.0
>> Checking sanity
>>     Checking GENERAL
>>     Checking MM
>>     Checking PB
>>     Checking GB
>>     Checking MS
>>
>> =>> Creating input
>>     Sander input
>>     PBSA input
>>
>> =>> Calculating energy / entropy contributions
>>     Calc contrib for ./snapshot_com.crd.1
>>         Calc MM/GB/SAS
>>         Generate PDB
>>         Center PDB
>>         Calc PBSA
>> $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>>         /u0/z/zz217/USG/amber/9.0/exe/pbsa -O -i pbsa.in -o
>> pbsa_com.1.out -c ./snapshot_com.crd.1 -p ./GNNQQNYMYRSB.prmtop not
>> successful
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>    }><(({*>
> __/
>
> Jordan MONNET
> Bachelor in Biology & Computer science
> University of Paris Diderot (Paris VII)
>
> http://monnet.jordan.free.fr/
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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