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.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.gmail.com>
> To: AMBER Mailing List <amber.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.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.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.gmail.com>
>> To: AMBER.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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
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>>
>
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Received on Wed Aug 19 2009 - 22:35:31 PDT
