Given this message in your output:
SA Bomb in sa_arc(): Allocation aborted
I would say that you are running out of memory on your computer to run this
PB calculation. I would suggest trying to run the calculation on a computer
with more RAM or estimate the PB energies by running a GB calculation
instead.
I hope that helps.
-Bill
On Wed, May 9, 2012 at 1:05 AM, Jyotsna Bhat <bhat.jyotsna.yahoo.com> wrote:
> I tried with python scripts of Amber11 but I got the same error
>
> --- On Tue, 5/8/12, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
> From: Ray Luo, Ph.D. <ray.luo.uci.edu>
> Subject: Re: [AMBER] MMPBSA calculation of large proteins
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Tuesday, May 8, 2012, 4:39 PM
>
> It won't matter which sander did you use to simulate the system ...
> I'm keeping my fingers crossed, :).
>
> Ray
>
> On Tue, May 8, 2012 at 3:02 AM, Jyotsna Bhat <bhat.jyotsna.yahoo.com>
> wrote:
> >
> > To Ray Luo,
> >
> > I have used amber10 while simulation run, will it affect the binding
> energy result if I use mmpbsa python scripts installed with amber11
> version. There may be different parameters applied in amber11 which will
> give different results with amber10 simulation systems
> >
> > --- On Mon, 5/7/12, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> >
> > From: Ray Luo, Ph.D. <ray.luo.uci.edu>
> > Subject: Re: [AMBER] MMPBSA calculation of large proteins
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Date: Monday, May 7, 2012, 5:15 PM
> >
> > Why not upgrade to the latest AmberTools? It's free and should resolve
> > the issue.
> >
> > All the best,
> > Ray
> >
> > Ray
> >
> > On Mon, May 7, 2012 at 9:31 AM, Jyotsna Bhat <bhat.jyotsna.yahoo.com>
> wrote:
> >> I have used Amber10 for MD run and further calculations. I am using
> perl scripts for mmpbsa.INPUT files
> >> for extraction of coordinates as follows:
> >> .GENERAL
> >> PREFIX snapshot
> >> PATH ./
> >> COMPLEX 1
> >> RECEPTOR 1
> >> LIGAND 1
> >> COMPT
> >> ../prmtop/complex_vac.prmtop
> >> RECPT ../prmtop/prot_vac.prmtop
> >> LIGPT ../prmtop/BIM.prmtop
> >> GC 1
> >> AS 0
> >> DC 0
> >> MM 0
> >> GB
> >> 0
> >> PB 0
> >> MS 0
> >> NM 0
> >> .MAKECRD
> >> BOX YES
> >> NTOTAL 9249
> >> NSTART 1
> >> NSTOP 999
> >> NFREQ
> >> 100
> >> NUMBER_LIG_GROUPS 1
> >> LSTART 9188
> >> LSTOP 9249
> >> NUMBER_REC_GROUPS 1
> >> RSTART 1
> >> RSTOP 9187
> >> .TRAJECTORY
> >> TRAJECTORY ../strip_mdcrd/2mBIM_nowat.mdcrd
> >> .PROGRAMS
> >> for binding energy calculation:
> >> .GENERAL
> >> PREFIX
> >> snapshot
> >> PATH ./
> >> #
> >> COMPLEX 1
> >> RECEPTOR 1
> >> LIGAND 1
> >> #
> >> COMPT ../prmtop/complex_vac.prmtop
> >> RECPT ../prmtop/prot_vac.prmtop
> >> LIGPT ../prmtop/BIM.prmtop
> >> #
> >> GC
> >> 0
> >> AS 0
> >> DC 0
> >> #
> >> MM 1
> >> GB 1
> >> 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
> >> .
> >> Extraction occurs with no problems but after running binding energy
> script it gives error as follows:
> >> /opt/amber10/exe/sander
> >> -O -i pbsa_com.in -o pbsa_com.1.out -c ./snapshot_com.crd.1 -p
> >> ../prmtop/complex_vac.prmtop not successful
> >>
> >> log file of binding energy calculation:
> >>
> >> =>> Init data
> >> Presuming executables of amber suite to be in /opt/amber10/exe
> >>
> >> =>> Reading input parameters
> >> Found PREFIX => snapshot
> >> Found PATH => ./
> >> Found COMPLEX => 1
> >> Found RECEPTOR => 1
> >> Found LIGAND => 1
> >> Found COMPT => ../prmtop/complex_vac.prmtop
> >> Found RECPT =>
> >> ../prmtop/prot_vac.prmtop
> >> Found LIGPT => ../prmtop/BIM.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
> >> 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
> >>
> >> pbsa_com.1.out:
> >>
> >> File Assignments:
> >> | MDIN: pbsa_com.in
> >> | MDOUT: pbsa_com.1.out
> >> |INPCRD:
> >> ./snapshot_com.crd.1
> >> | PARM: ../prmtop/complex_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,
> >> ivcap =
> >> 0, cutcap = -1,
> >> xcap = 0, ycap = 0, zcap = 0
> >> idecomp=
> >> 0,
> >> &end
> >>
> >> &pb
> >> epsin = 1.0, epsout = 80.0,
> >> istrng = 0.0, radiopt =
> >> 0,
> >> sprob = 1.4, space = 0.5,
> >> maxitn = 1000, npopt = 1, dbfopt = 1,
> >> cavity_surften = 0.0072, fillratio = 4.00,
> >> cavity_offset = 0.00,
> >> npbverb= 1
> >> &end
> >>
> >>
> >>
> --------------------------------------------------------------------------------
> >> 1. RESOURCE USE:
> >>
> --------------------------------------------------------------------------------
> >>
> >> | Flags:
> >> | New format PARM file being parsed.
> >> | Version = 1.000 Date = 08/09/11 Time = 22:39:42
> >> NATOM = 9249 NTYPES = 18 NBONH = 4578 MBONA = 4783
> >> NTHETH =
> >> 10490 MTHETA = 6457 NPHIH = 19824 MPHIA = 15978
> >> NHPARM = 0 NPARM = 0 NNB = 51187 NRES = 579
> >> NBONA = 4783 NTHETA = 6457 NPHIA = 15978 NUMBND = 66
> >> NUMANG = 132 NPTRA = 49 NATYP = 47 NPHB = 0
> >> IFBOX = 0 NMXRS = 62 IFCAP = 0 NEXTRA = 0
> >> NCOPY = 0
> >>
> >> Implicit solvent radii are modified Bondi radii
> >> (mbondi)
> >>
> >> | Memory Use Allocated
> >> | Real 592745
> >> | Hollerith 56075
> >> | Integer 500704
> >> | Max Pairs 1
> >> | nblistReal
> >> 0
> >> | nblist Int 0
> >> | Total 6805 kbytes
> >> | Duplicated 0 dihedrals
> >> | Duplicated 0 dihedrals
> >>
> >>
> --------------------------------------------------------------------------------
> >> 2. CONTROL DATA FOR THE
> >> RUN
> >>
> --------------------------------------------------------------------------------
> >>
> >>
> >>
> >> 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: 10405125 2247507 42772001
> >>
> >> no. of atoms processed in PB initialization: 9249
> >> NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP
> RADI
> >> 1 LYS N N3 0.096600 0.746100 0.862600 1.550000
> 1.550000
> >> 2 LYS H1 H 0.216500
> >> 0.000000 0.000000 1.300000 1.300000
> >> 3 LYS H2 H 0.216500 0.000000 0.000000 1.300000
> 1.300000
> >> 4 LYS H3 H 0.216500 0.000000 0.000000 1.300000
> 1.300000
> >> 5 LYS CA CT -0.001500 0.116500 1.661800 1.700000
> 1.700000
> >> 6 LYS HA HP 0.118000 0.000000 0.000000 1.300000
> 1.300000
> >> 7 LYS CB CT 0.021200 0.077800 0.213700 1.700000
> 1.700000
> >> 8 LYS HB2 HC 0.028300 0.000000
> >> 0.000000 1.300000 1.300000
> >> .
> >> .
> >> .
> >> 246 BIM C20 ca -0.101600 0.043300 -0.012800 1.700000 1.700000
> >> 9247 BIM H12 ha 0.144900 0.144900 0.144900 1.300000
> 1.300000
> >> 9248 BIM C21 ca -0.191300 -0.065000 -0.108300 1.700000
> 1.700000
> >> 9249 BIM H13 ha 0.126300 0.126300 0.126300 1.300000
> 1.300000
> >>
> >> total system charges (+/-) for PB -2.9998 1123.8366
> -1126.8364
> >> cavity_surften = 0.0072 cavity_offset =
> >> 0.0000
> >>
> >> SAS Surface: surface dots generated: 366
> >> | INFO: Old style inpcrd file read
> >>
> --------------------------------------------------------------------------------
> >> 3. ATOMIC COORDINATES AND VELOCITIES
> >>
> --------------------------------------------------------------------------------
> >>
> >> trajectory generated by ptraj
> >> 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 4087009
> >> NB-update: atom-based nb list 905095
> >>
> >>
> >> ======== Setting up Grid Parameters ========
> >> Using bounding box for grid setup
> >> Bounding Box Center: 67.500 73.000 67.500
> >> Xmin, Xmax, Xmax-Xmin: 20.518 114.427 93.909
> >> Ymin, Ymax, Ymax-Ymin: 17.394 128.517 111.123
> >> Zmin, Zmax, Zmax-Zmin: 26.562 108.482 81.920
> >> beginning box center at level 1
> >> 67.500 73.000 67.500
> >> beginning box center at level 2 67.500 73.000 67.500
> >> Grid dimension at level 1 95 113 83
> >> Grid origin corrected at level 1 -124.500 -155.000 -100.500
> >> Grid dimension at level 2 203 237 179
> >> Grid origin corrected at level 2 16.500 13.500 22.500
> >> SA surface: setting up working radii
> >> SA surface: found nonzero radii 9249
> >> Number of SA srf points exposed133796
> >> SA Bomb in sa_arc(): Allocation
> >> aborted 0 0 0
> >> 0 41
> >>
> >> I
> >> tried same process by removing calcium zinc ions which are present in
> >> respective system but error remains the same. I also tried considering
> >> ions as ligand, as receptor but no positive result. I also reduced the
> >> protein size by abducting regulatory domain and keeping only active
> >> domain but I could not form the neccessary topology files as removal of
> >> part of protein cause imbalance of hydrogens due to loss of peptide
> >> bond. tleap adds some extra hydrogens on its own but they are not
> >> present in original mdcrd trjectory file so i could not use such
> >> topology files for calculations.
> >>
> >> Than you so much for your consideration.
> >> Regards,
> >> Jyotsna
> >>
> >>
> >>
> >> --- On Mon, 5/7/12, Jason Swails <jason.swails.gmail.com> wrote:
> >>
> >> From: Jason Swails <jason.swails.gmail.com>
> >> Subject: Re: [AMBER] MMPBSA calculation of large proteins
> >> To: "AMBER Mailing List" <amber.ambermd.org>
> >> Date: Monday, May 7, 2012, 2:14 PM
> >>
> >> We need more information.
> >>
> >> What version of Amber/AmberTools are you using? Which MM/PBSA script
> are
> >> you using? What is your input file? What is your *exact* error (not
> just
> >> part of your error). Based on the provided information it's impossible
> to
> >> debug any further.
> >>
> >> All the best,
> >> Jason
> >>
> >> On Mon, May 7, 2012 at 2:58 AM, Jyotsna Bhat <bhat.jyotsna.yahoo.com>
> wrote:
> >>
> >>> Dear AMBER users,
> >>> I am trying to run MMPBSA script on 10 ns simulation trajectory.(
> My
> >>> protein-ligand complex system has 579 residues. It is a multidomain
> >>> protein; active domain and regulatory domain are situated far away from
> >>> each other, but linked by a large loop. Ligand is present in an active
> >>> domain). Extraction of coordinates is done successfully but during
> binding
> >>> energy calculation job gets aborted at first coordinate only with the
> error
> >>> "complex_vac.prmtop not successful".I have tried the adjustment with
> >>> fillratio (2,3 or 4) but it didn't help. Waiting for suggestions
> >>> Thank you.Jyotsna
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Candidate
> >> 352-392-4032
> >> _______________________________________________
> >> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed May 09 2012 - 06:30:04 PDT
