My suggestion is to upgrade to the latest AmberTool ... this shouldn't
be a problem any more for most systems.
Ray
On Wed, May 9, 2012 at 6:08 AM, Bill Miller III <brmilleriii.gmail.com> wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> 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
> _______________________________________________
> AMBER mailing list
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Received on Wed May 09 2012 - 09:30:04 PDT
