AMBER Archive (2009)

Subject: Re: [AMBER] MM_PBSA not successful

From: workalemahu berhanu (wgberhanu_at_gmail.com)
Date: Fri Aug 14 2009 - 23:22:57 CDT

Dear Qinghua

I have below the output files .

Thank you

 snapshot_com.all.out

MM
GB
PB
MS
1
 BOND = 205.9547 ANGLE = 500.8292 DIHED = 874.2771
 VDWAALS = -556.5644 EEL = -5494.9002 EGB = -1897.5408
 1-4 VDW = 225.8409 1-4 EEL = 658.6870 RESTRAINT = 0.0000

sander_com.in
File generated by mm_pbsa.pl. Using MM GB
 &cntrl
  ntf = 1, ntb = 0, dielc = 1.0,
  idecomp= 0,
  igb = 2, saltcon= 0.00,
  offset = 0.09,
  intdiel= 1.0, extdiel= 80.0,
  gbsa = 0, surften= 1.0,
  cut = 999.0, nsnb = 99999,
  scnb = 2.0, scee = 1.2,

  imin = 1, maxcyc = 1, ncyc = 0,
 &end

sander_lig.in
File generated by mm_pbsa.pl. Using MM GB
 &cntrl
  ntf = 1, ntb = 0, dielc = 1.0,
  idecomp= 0,
  igb = 2, saltcon= 0.00,
  offset = 0.09,
  intdiel= 1.0, extdiel= 80.0,
  gbsa = 0, surften= 1.0,
  cut = 999.0, nsnb = 99999,
  scnb = 2.0, scee = 1.2,

  imin = 1, maxcyc = 1, ncyc = 0,
 &end
sander_rec.in
File generated by mm_pbsa.pl. Using MM GB
 &cntrl
  ntf = 1, ntb = 0, dielc = 1.0,
  idecomp= 0,
  igb = 2, saltcon= 0.00,
  offset = 0.09,
  intdiel= 1.0, extdiel= 80.0,
  gbsa = 0, surften= 1.0,
  cut = 999.0, nsnb = 99999,
  scnb = 2.0, scee = 1.2,

  imin = 1, maxcyc = 1, ncyc = 0,
 &end
pbsa.in
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

mdinfo

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -5.4834E+03 1.8389E+01 1.0540E+02 CE2 636

 BOND = 205.9547 ANGLE = 500.8292 DIHED = 874.2771
 VDWAALS = -556.5644 EEL = -5494.9002 EGB = -1897.5408
 1-4 VDW = 225.8409 1-4 EEL = 658.6870 RESTRAINT = 0.0000
~

On Fri, Aug 14, 2009 at 10:43 PM, Qinghua Liao<fantasticqhl_at_yahoo.com> wrote:
> Dear Sir,
>
> If so, I think you should check the other output files to find some clues about the error. or you can show us those output files.
> Good luck!
>
> Qinghua
>
>
>
>
> ________________________________
> From: workalemahu berhanu <wgberhanu_at_gmail.com>
> To: AMBER Mailing List <amber_at_ambermd.org>
> Sent: Saturday, August 15, 2009 10:36:39 AM
> Subject: Re: [AMBER] MM_PBSA not successful
>
> Dear Qinghua
>
> Hi
> I introduced a line with fillratio=3.0 or 4.0 in the file pbsa.in. As
> you explained in the mail archive
> (http://archive.ambermd.org/200905/0326.html). The problem is still
> there
>
> mikre_at_nid00235:~/PRION/MMPBSA> 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
>
> GNNQQNYMYRSB is the complex
>
> Thank you
>
> On Fri, Aug 14, 2009 at 9:20 PM, Qinghua Liao<fantasticqhl_at_yahoo.com> wrote:
>> Hi,
>>
>> Maybe you should change the value of fillratio from default 2.0 to 3.0 or 4.0, you can have a try.
>>
>> Good luck!
>>
>> Qinghua
>>
>>
>>
>>
>> ________________________________
>> From: workalemahu berhanu <wgberhanu_at_gmail.com>
>> To: AMBER_at_ambermd.org
>> Sent: Saturday, August 15, 2009 5:45:41 AM
>> Subject: [AMBER] MM_PBSA not successful
>>
>> 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
>>
>> _______________________________________________
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>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
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>>
>
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