This could mean that you do not have sufficient memory on your computer to
run this calculation. Try running the calculation with a computer that can
allocate more memory. PB calculations can be memory intensive for large
systems.
I hope that helps.
-Bill
On Wed, May 9, 2012 at 2:53 AM, jyoti alyan <jyotialyan.gmail.com> wrote:
> Dear all,
> I am running the binding free energy calculation on Amber10 using
> mm_pbsa.pl. I extracted all the coordinates correctly, but when i run
> the command
> mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>
> i got the following error
> /opt/amber10/exe/sander -O -i pbsa_com.in -o pbsa_com.1.out -c
> ./snapshot_com.crd.1 -p ./1nca_zmr_vac.prmtop not successful
>
> I tried with different fillratio (2.0, 3.0, 4.0) but the problem is still
> there.
>
> My input files are:
>
> 1. extract_coords.mmpbsa
> .GENERAL
> PREFIX snapshot
> PATH ./
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./1nca_zmr_vac.prmtop
> RECPT ./recep.prmtop
> LIGPT ./zmr.prmtop
> GC 1
> AS 0
> DC 0
> MM 0
> GB 0
> PB 0
> MS 0
> NM 0
> .MAKECRD
> BOX YES
> NTOTAL 119005
> NSTART 1
> NSTOP 999
> NFREQ 1
> NUMBER_LIG_GROUPS 1
> LSTART 12553
> LSTOP 12597
> NUMBER_REC_GROUPS 1
> RSTART 1
> RSTOP 12552
> .TRAJECTORY
> TRAJECTORY ./prod1.mdcrd
> .PROGRAMS
>
> 2. binding_energy.mmpbsa
> .GENERAL
> PREFIX snapshot
> PATH ./
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./1nca_zmr_vac.prmtop
> RECPT ./recep.prmtop
> LIGPT ./zmr.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
> .PROGRAMS
>
> and out files are
>
> 1. extract_coords.log
> 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 => ./1nca_zmr_vac.prmtop
> Found RECPT => ./recep.prmtop
> Found LIGPT => ./zmr.prmtop
> Found GC => 1
> Found AS => 0
> Found DC => 0
> Found MM => 0
> Found GB => 0
> Found PB => 0
> Found MS => 0
> Found NM => 0
> Found BOX => YES
> Found NTOTAL => 119005
> Found NSTART => 1
> Found NSTOP => 999
> Found NFREQ => 1
> Found NUMBER_LIG_GROUPS => 1
> Found LSTART => 12553
> Found LSTOP => 12597
> Found NUMBER_REC_GROUPS => 1
> Found RSTART => 1
> Found RSTOP => 12552
> Found TRAJECTORY => ./prod1.mdcrd
>
> =>> 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 GC
> Checking TRAJ
>
> =>> Creating input
> make_crd input
>
> =>> Creating coordinates
> Executing makecrd
>
> Amber8 Module: make_crg_hg
>
> usage: make_crd_hg < trajectory_file
> Box info found:
>
> ...........................................................................................
> ......................
>
> 2. binding_energy.log
> =>> 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 => ./1nca_zmr_vac.prmtop
> Found RECPT => ./recep.prmtop
> Found LIGPT => ./zmr.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
>
> 3. pbsa_com.1.out
>
> -------------------------------------------------------
> Amber 10 SANDER 2008
> -------------------------------------------------------
>
> | Run on 05/03/2012 at 19:26:56
> [-O]verwriting output
>
> File Assignments:
> | MDIN: pbsa_com.in
> | MDOUT: pbsa_com.1.out
> |INPCRD: ./snapshot_com.crd.1
> | PARM: ./1nca_zmr_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 = 01/16/12 Time = 17:03:01
> NATOM = 12597 NTYPES = 16 NBONH = 6169 MBONA = 6593
> NTHETH = 13963 MTHETA = 8985 NPHIH = 27219 MPHIA = 22476
> NHPARM = 0 NPARM = 0 NNB = 69551 NRES = 826
> NBONA = 6593 NTHETA = 8985 NPHIA = 22476 NUMBND = 62
> NUMANG = 130 NPTRA = 54 NATYP = 45 NPHB = 0
> IFBOX = 0 NMXRS = 45 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> Implicit solvent radii are modified Bondi radii (mbondi)
>
> | Memory Use Allocated
> | Real 807106
> | Hollerith 76410
> | Integer 678464
> | Max Pairs 1
> | nblistReal 0
> | nblist Int 0
> | Total 9254 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: 14171625 3061071 79342205
>
> no. of atoms processed in PB initialization: 12597
>
> .........................................................................................
> ..................
> total system charges (+/-) for PB -1.0003 1580.8984 -1581.8987
> 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
>
> --------------------------------------------------------------------------------
>
>
> 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 6731332
> NB-update: atom-based nb list 1421425
>
>
> ======== Setting up Grid Parameters ========
> Using bounding box for grid setup
> Bounding Box Center: 45.000 50.500 62.500
> Xmin, Xmax, Xmax-Xmin: 9.333 81.080 71.747
> Ymin, Ymax, Ymax-Ymin: 4.899 95.891 90.992
> Zmin, Zmax, Zmax-Zmin: 7.799 117.046 109.247
> beginning box center at level 1 45.000 50.500 62.500
> beginning box center at level 2 45.000 50.500 62.500
> Grid dimension at level 1 73 93 111
> Grid origin corrected at level 1 -103.000 -137.500 -161.500
> Grid dimension at level 2 157 197 233
> Grid origin corrected at level 2 5.500 1.000 4.000
> SA surface: setting up working radii
> SA surface: found nonzero radii 12597
> Number of SA srf points exposed129344
> SA Bomb in sa_arc(): Allocation aborted 0 0
> 41
> 0 0
>
> Thank you
>
> Jyoti Alyan
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 06:30:05 PDT
