Dear AMBER user,
I think I have exactly the same problem with this post. I used Amber 11,
and mmpbsa.pl script to calculate the binding free energy for a
protein-ligand complex.
It actually did not show any specific error in the log file, but the
calculation just terminated (at com.6).
According to the archive posts, the problem may be the memory -involved.
Do you have any idea how to overcome it? Please help.
.Jason Swails: will the mmpbsa.py solve the memory problem? I am using
AmberTools1.5, and as you suggested to some friend in the AMBER list to use
mmpbsa.py (AmberTools13), can I ask a trivial question (sorry I am one of
the dummies) that if I need to install AmberTools13, I have to start from
scratch the whole process of installing Amber11 and CUDA??? If it's true,
oh god, a nightmare!!!
Thank you.
Regards,
Chinh
-----------------------------------------------
This is the error I got:
*Use of uninitialized value $inp in concatenation (.) or string at
/home/pdca/software/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.*
*Use of uninitialized value $inp in concatenation (.) or string at
/home/pdca/software/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.*
*Use of uninitialized value $inp in concatenation (.) or string at
/home/pdca/software/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.*
*
*
* Unit 5 Error on OPEN: pbsa_com.in
*
* /home/pdca/software/amber11/bin/sander -O -i pbsa_com.in -o
pbsa_com.6.out -c ./snapshot_osel_com.crd.6 -p ./NA_osel_noWAT.prmtop not
successful*
* For details see:
http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful*
And this is the log file content:
*=>> Init data*
* Presuming executables of amber suite to be in
/home/pdca/software/amber11/bin*
*
*
*=>> Reading input parameters*
* Found PREFIX => snapshot_osel*
* Found PATH => ./*
* Found COMPLEX => 1*
* Found RECEPTOR => 1*
* Found LIGAND => 1*
* Found COMPT => ./NA_osel_noWAT.prmtop*
* Found RECPT => ./NA.prmtop*
* Found LIGPT => ./osel.prmtop*
* Found GC => 0*
* Found AS => 0*
* Found DC => 0*
* Found MM => 1*
* Found GB => 1*
* 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*
* Setting START to default 1*
* Setting STOP to default 10e10*
* Setting OFFSET to default 1*
* Setting VERBOSE to default 0*
* Setting PARALLEL to default 0*
* Checking MM*
* Checking PB*
* Checking GB*
* Checking MS*
*
*
*=>> Creating input*
* Sander input*
* PBSA input*
*
*
*=>> Calculating energy / entropy contributions*
* Calc contrib for ./snapshot_osel_com.crd.1*
* Checking atom numbers*
* Calc MM/GB/SAS*
* Generate PDB*
* Center PDB*
* Calc PBSA*
* Generate PQR*
* Calc MS*
* Analyzing 1*
* Ana MM/GB/SAS*
* Ana PBSA*
* Ana MS*
* Calc contrib for ./snapshot_osel_com.crd.2*
* Calc MM/GB/SAS*
* Generate PDB*
* Center PDB*
* Calc PBSA*
* Generate PQR*
* Calc MS*
* Analyzing 2*
* Ana MM/GB/SAS*
* Ana PBSA*
* Ana MS*
* Calc contrib for ./snapshot_osel_com.crd.3*
* Calc MM/GB/SAS*
* Generate PDB*
* Center PDB*
* Calc PBSA*
* Generate PQR*
* Calc MS*
* Analyzing 3*
* Ana MM/GB/SAS*
* Ana PBSA*
* Ana MS*
* Calc contrib for ./snapshot_osel_com.crd.4*
* Calc MM/GB/SAS*
* Generate PDB*
* Center PDB*
* Calc PBSA*
* Generate PQR*
* Calc MS*
* Analyzing 4*
* Ana MM/GB/SAS*
* Ana PBSA*
* Ana MS*
* Calc contrib for ./snapshot_osel_com.crd.5*
* Calc MM/GB/SAS*
* Generate PDB*
* Center PDB*
* Calc PBSA*
* Generate PQR*
* Calc MS*
* Analyzing 5*
* Ana MM/GB/SAS*
* Ana PBSA*
* Ana MS*
* Calc contrib for ./snapshot_osel_com.crd.6*
* Calc MM/GB/SAS*
* Generate PDB*
* Center PDB*
* Calc PBSA*
*
*
*
*
The pbsa_com.6 just came with only 1 line:
*
*
*Unit 5 Error on OPEN: pbsa_com.in
*
*
*
And this is the sander_com.6:
*
*
*
*
* -------------------------------------------------------*
* Amber 11 SANDER 2010*
* -------------------------------------------------------*
*
*
*| Run on 06/11/2013 at 14:50:35*
* [-O]verwriting output*
*
*
*File Assignments:*
*| MDIN: sander_com.in
*
*| MDOUT: sander_com.6.out
*
*|INPCRD: ./snapshot_osel_com.crd.6
*
*| PARM: ./NA_osel_noWAT.prmtop
*
*|RESTRT: restrt
*
*| REFC: refc
*
*| MDVEL: mdvel
*
*| MDEN: mden
*
*| MDCRD: mdcrd
*
*|MDINFO: mdinfo
*
*| MTMD: mtmd
*
*|INPDIP: inpdip
*
*|RSTDIP: rstdip
*
*
*
*|INPTRA: inptraj
*
*|*
*
*
* Here is the input file:*
*
*
*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,
*
*
*
* imin = 1, maxcyc = 1, ncyc = 0,
*
* &end
*
*
--------------------------------------------------------------------------------
*
*
*
*| Flags:
*
*| New format PARM file being parsed.*
*| Version = 1.000 Date = 06/10/13 Time = 13:45:39*
* NATOM = 7149 NTYPES = 15 NBONH = 3495 MBONA = 3743*
* NTHETH = 7918 MTHETA = 5099 NPHIH = 15917 MPHIA = 12789*
* NHPARM = 0 NPARM = 0 NNB = 39384 NRES = 466*
* NBONA = 3743 NTHETA = 5099 NPHIA = 12789 NUMBND = 60*
* NUMANG = 131 NPTRA = 57 NATYP = 40 NPHB = 0*
* IFBOX = 0 NMXRS = 51 IFCAP = 0 NEXTRA = 0*
* NCOPY = 0*
*
*
* Implicit solvent radii are modified Bondi radii (mbondi)
*
*
*
*| Memory Use Allocated*
*| Real 479621*
*| Hollerith 21915*
*| Integer 396058*
*| Max Pairs 1*
*| nblistReal 0*
*| nblist Int 0*
*| Total 5379 kbytes*
*
*
*| Note: 1-4 EEL scale factors are being read from the topology file.*
*
*
*| Note: 1-4 VDW scale factors are being read from the topology file.*
*| Duplicated 0 dihedrals*
*| Duplicated 0 dihedrals*
*
*
*.....*
*
*
*
*
* NSTEP ENERGY RMS GMAX NAME NUMBER*
* 1 2.6521E+06 1.3779E+04 6.1988E+05 N 7099*
*
*
* BOND = 2094141.2372 ANGLE = 8044.6655 DIHED =
4983.0467*
* VDWAALS = 546253.5868 EEL = -32906.3352 EGB =
-4476.2307*
* 1-4 VDW = 18536.0400 1-4 EEL = 17512.1509 RESTRAINT =
0.0000*
*
*
*
*
* Maximum number of minimization cycles reached.*
*
*
*
*
* FINAL RESULTS*
*
*
*
*
*
*
* NSTEP ENERGY RMS GMAX NAME NUMBER*
* 1 2.6521E+06 1.3779E+04 6.1988E+05 N 7099*
*
*
* BOND = 2094141.2372 ANGLE = 8044.6655 DIHED =
4983.0467*
* VDWAALS = 546253.5868 EEL = -32906.3352 EGB =
-4476.2307*
* 1-4 VDW = 18536.0400 1-4 EEL = 17512.1509 RESTRAINT =
0.0000*
*
*
*
--------------------------------------------------------------------------------
*
* 5. TIMINGS*
*
--------------------------------------------------------------------------------
*
*
*
*| Read coords time 0.01 ( 0.11% of Total)*
*| Calc gb radii 1.14 (14.68% of Gen B)*
*| Calc gb diag 2.13 (27.32% of Gen B)*
*| Calc gb off-diag 4.52 (58.00% of Gen B)*
*| Gen Born time 7.79 (100.0% of Nonbo)*
*| Nonbond force 7.79 (99.80% of Force)*
*| Bond/Angle/Dihedral 0.02 ( 0.20% of Force)*
*| Force time 7.80 (100.0% of Runmd)*
*| Runmd Time 7.80 (98.33% of Total)*
*| Other 0.12 ( 1.57% of Total)*
*| Total time 7.94 (100.0% of ALL )*
*
*
*| Highest rstack allocated: 0*
*| Highest istack allocated: 0*
*| Job began at 14:50:35.115 on 06/11/2013*
*| Setup done at 14:50:35.213 on 06/11/2013*
*| Run done at 14:50:43.051 on 06/11/2013*
*| wallclock() was called 45 times*
*
*
*
*
On Mon, Aug 22, 2011 at 8:31 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Okay, based on your attached output file. It seems that your computer
> does not have enough memory for you to run mmpbsa with such a small
> grid spacing ... please change scale from 4 to 2 and try again ...
>
> All the best,
> Ray
>
> On Mon, Aug 22, 2011 at 8:12 PM, Esam Tolba <eatolba.gmail.com> wrote:
> >
> > THanks for help
> >
> >
> > ---------- Forwarded message ----------
> > From: Ray Luo, Ph.D. <ray.luo.uci.edu>
> > Date: Mon, Aug 22, 2011 at 1:58 PM
> > Subject: Re: [AMBER] Error in mm_pbsa
> > To: AMBER Mailing List <amber.ambermd.org>
> >
> >
> > Can you email me off the list, the file "pbsa_com.1.out"? It's really
> > hard to understand what's going on only with the info in the log file
> > ...
> >
> > All the best,
> > Ray
> >
> > On Mon, Aug 22, 2011 at 7:38 PM, Esam Tolba <eatolba.gmail.com> wrote:
> >> Dear Amber Team
> >> i am using mm_pbsa in determining the binding energy and i made the
> >> snapshot
> >> step with out any errors but when i tried calculation of the energy i
> got
> >> this error:
> >>
> >> =>> Init data
> >> Presuming executables of amber suite to be in
> >> /usr/local/Amber/Amber11/serial-gnu/amber11/bin
> >>
> >> =>> Reading input parameters
> >> Found PREFIX => trial_1
> >> Found PATH => ./
> >> Found COMPLEX => 1
> >> Found RECEPTOR => 1
> >> Found LIGAND => 1
> >> Found COMPT => ./1KPV_complex_wo_salt.top
> >> Found RECPT => ./1KPV_all_acceptor_wo_salt.top
> >> Found LIGPT => ./1KPV_all_ligand_wo_salt.top
> >> Found GC => 0
> >> Found AS => 0
> >> Found DC => 0
> >> Found MM => 1
> >> Found GB => 1
> >> 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 => 4.0
> >> Found LINIT => 500
> >> Found PRBRAD => 1.6
> >> Found RADIOPT => 0
> >> Found FOCUS => 0
> >> Found PERFIL => 80.0
> >> Found CHARGE => ./my_amber94_delphi.crg
> >> Found SIZE => ./my_parse_delphi.siz
> >> Found SURFTEN => 0.005
> >> Found SURFOFF => 0.0
> >> 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
> >> Found DELPHI => /home/gohlke/src/delphi.98/exe/delphi
> >>
> >> =>> Checking sanity
> >> Checking GENERAL
> >> Setting START to default 1
> >> Setting STOP to default 10e10
> >> Setting OFFSET to default 1
> >> Setting VERBOSE to default 0
> >> Setting PARALLEL to default 0
> >> Checking MM
> >> Checking PB
> >> Checking GB
> >> Checking MS
> >>
> >> =>> Creating input
> >> Sander input
> >> PBSA input
> >> Use of uninitialized value $inp in concatenation (.) or string at
> >> /usr/local/Amber/Amber11/serial-gnu/amber11/src/mm_pbsa/
> >> mm_pbsa_createinput.pm line 596.
> >> Use of uninitialized value $inp in concatenation (.) or string at
> >> /usr/local/Amber/Amber11/serial-gnu/amber11/src/mm_pbsa/
> >> mm_pbsa_createinput.pm line 596.
> >> Use of uninitialized value $inp in concatenation (.) or string at
> >> /usr/local/Amber/Amber11/serial-gnu/amber11/src/mm_pbsa/
> >> mm_pbsa_createinput.pm line 596.
> >>
> >> =>> Calculating energy / entropy contributions
> >> Calc contrib for ./trial_1_com.crd.1
> >> Checking atom numbers
> >> Calc MM/GB/SAS
> >> Generate PDB
> >> Center PDB
> >> Calc PBSA
> >> /usr/local/Amber/Amber11/serial-gnu/amber11/bin/sander -O -i
> >> pbsa_com.in -o pbsa_com.1.out -c ./trial_1_com.crd.1 -p
> >> ./1KPV_complex_wo_salt.top not successful
> >> For details see:
> >> http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful
> >>
> >>
> >> Best Regards,
> >> *Esam *
> >> _______________________________________________
> >> 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
> >
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jun 11 2013 - 02:30:03 PDT
