AMBER Archive (2009)

Subject: Re: [AMBER] Error in MM PBSA

From: Ray Luo (ray.luo_at_uci.edu)
Date: Sun Jun 07 2009 - 14:17:30 CDT

Fix fillratio = 2 AND set space=0.75, 1.00, 1.25, and so on until the
error message goes away.

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

Vikas Sharma wrote:
> Dear Dr. Ray Luo,
> I set the fill ratio to 1, 1.75 &2...but i found errors..
>
>
> the message for fillratio =3.0 was same as that for 2.0
>
>
> what should i do next???
>
> 1. fillratio = 1.0:
>
>
> Amber 10
> SANDER 2008
> -------------------------------------------------------
>
> | Run on 06/07/2009 at 19:37:01
> [-O]verwriting output
>
> File Assignments:
> | MDIN: pbsa_com.in
> | MDOUT: pbsa_com.1.out
> |INPCRD: /home/bharatam/amberresults_w/amberresults31/snapshot_com.crd.1
> | PARM:
> /home/bharatam/amberresults_w/amb31/A31.prmtop
> |RESTRT: restrt
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: mdcrd
> |MDINFO: mdinfo
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
> |INPTRA: inptraj
> |
>
> 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, cavity_offset = 0.00,
> pbtemp = 300.0,
> fillratio = 1.0 npbverb= 1
> &end
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> | Flags:
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/25/09 Time
> = 15:24:22
> NATOM = 3777 NTYPES = 14 NBONH = 1904 MBONA = 1908
> NTHETH = 4330 MTHETA = 2563 NPHIH = 8175 MPHIA = 5873
> NHPARM = 0 NPARM = 0 NNB = 20879 NRES = 224
> NBONA = 1908 NTHETA = 2563 NPHIA = 5873 NUMBND = 52
> NUMANG = 108 NPTRA = 51 NATYP = 39 NPHB = 0
> IFBOX = 0 NMXRS = 44 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> Implicit solvent radii are modified
> Bondi radii (mbondi)
>
> | Memory Use Allocated
> | Real 242174
> | Hollerith 22888
> | Integer 213271
> | Max Pairs 1
> | nblistReal 0
> | nblist Int 0
> | Total 2814 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: 4249125 917811 7132865
> NB-update: residue-based nb list 1847160
> NB-update: atom-based nb list 378579
>
>
> ======== Setting up Grid Parameters
> ========
> Using bounding box for grid setup
> Bounding Box Center: 41.500 44.500 31.500
> Xmin, Xmax, Xmax-Xmin: 7.128 75.695 68.567
> Ymin, Ymax, Ymax-Ymin: 7.043 82.154 75.111
> Zmin, Zmax, Zmax-Zmin: 5.392 57.882 52.490
> beginning box center at level 1 41.500 44.500 31.500
> beginning box center at level 2 41.500 44.500 31.500
> Grid dimension at level 1 19 21 15
> Grid origin corrected at level 1 1.500 0.500 -0.500
> Grid dimension at level 2 151 165 119
> Grid origin corrected at level 2 3.500 3.000 1.500
> PB Bomb in setgrd(): focusing grid too large 2
> reset fillratio to a larger number 1.000
>
>
> 2. fillratio=1.75
>
>
> 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, cavity_offset = 0.00,
> pbtemp = 300.0,
> fillratio = 1.75 npbverb= 1
> &end
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> | Flags:
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/25/09 Time
> = 15:24:22
> NATOM = 3777 NTYPES = 14 NBONH = 1904 MBONA = 1908
> NTHETH = 4330 MTHETA = 2563 NPHIH = 8175 MPHIA = 5873
> NHPARM = 0 NPARM = 0 NNB = 20879 NRES = 224
> NBONA = 1908 NTHETA = 2563 NPHIA = 5873 NUMBND = 52
> NUMANG = 108 NPTRA = 51 NATYP = 39 NPHB = 0
> IFBOX = 0 NMXRS = 44 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> Implicit solvent radii are modified
> Bondi radii (mbondi)
>
> | Memory Use Allocated
> | Real 242174
> | Hollerith 22888
> | Integer 213271
> | Max Pairs 1
> | nblistReal 0
> | nblist Int 0
> | Total 2814 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: 4249125 917811 7132865
>
> no. of atoms processed in PB
> initialization: 3777
> NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI
> 1 MET N N3 0.159200 0.754400 0.888100 1.550000 1.550000
> 2 MET H1 H 0.198400 0.000000 0.000000 1.300000 1.300000
> 3 MET H2 H 0.198400 0.000000 0.000000 1.300000 1.300000
> 4 MET H3 H 0.198400 0.000000 0.000000 1.300000 1.300000
> 5 MET CA CT 0.022100 0.133700 1.611900 1.700000 1.700000
> 6 MET HA HP 0.111600 0.000000 0.000000 1.300000 1.300000
> 7 MET CB CT 0.086500 0.111500 0.337000
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> NB-update: residue-based nb list 1383768
> NB-update: atom-based nb list 53172
>
>
> ======== Setting up Grid Parameters
> ========
> Using bounding box for grid setup
> Bounding Box Center: 47.000 43.500 29.000
> Xmin, Xmax, Xmax-Xmin: -6.933 100.641 107.574
> Ymin, Ymax, Ymax-Ymin: -18.558 105.341 123.899
> Zmin, Zmax, Zmax-Zmin: -29.798 88.266 118.064
> beginning box center at level 1 47.000 43.500 29.000
> beginning box center at level 2 47.000 43.500 29.000
> Grid dimension at level 1 49 55 53
> Grid origin corrected at level 1 -53.000 -68.500 -79.000
> Grid dimension at level 2 229 263 251
> Grid origin corrected at level 2 -10.500 -22.500 -34.000
> SA surface: setting up working
> radii
> SA surface: found nonzero radii 3777
> Number of SA srf points exposed455488
> SA Bomb in sa_arc(): Allocation
> aborted 0 0 41
> 0 0
> 3. fillratio=2.0
>
>
> 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, cavity_offset = 0.00,
> pbtemp = 300.0,
> fillratio = 2.0 npbverb= 1
> &end
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> | Flags:
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/25/09 Time
> = 15:24:22
> NATOM = 3777 NTYPES = 14 NBONH = 1904 MBONA = 1908
> NTHETH = 4330 MTHETA = 2563 NPHIH = 8175 MPHIA = 5873
> NHPARM = 0 NPARM = 0 NNB = 20879 NRES = 224
> NBONA = 1908 NTHETA = 2563 NPHIA = 5873 NUMBND = 52
> NUMANG = 108 NPTRA = 51 NATYP = 39 NPHB = 0
> IFBOX = 0 NMXRS = 44 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> Implicit solvent radii are modified
> Bondi radii (mbondi)
>
> | Memory Use Allocated
> | Real 242174
> | Hollerith 22888
> | Integer 213271
> | Max Pairs 1
> | nblistReal 0
> | nblist Int 0
> | Total 2814 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: 4249125 917811 7132865
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> NB-update: residue-based nb list 1383768
> NB-update: atom-based nb list 53172
>
>
> ======== Setting up Grid Parameters
> ========
> Using bounding box for grid setup
> Bounding Box Center: 47.000 43.500 29.000
> Xmin, Xmax, Xmax-Xmin: -6.933 100.641 107.574
> Ymin, Ymax, Ymax-Ymin: -18.558 105.341 123.899
> Zmin, Zmax, Zmax-Zmin: -29.798 88.266 118.064
> beginning box center at level 1 47.000 43.500 29.000
> beginning box center at level 2 47.000 43.500 29.000
> Grid dimension at level 1 55 63 61
> Grid origin corrected at level 1 -65.000 -84.500 -95.000
> Grid dimension at level 2 229 263 251
> Grid origin corrected at level 2 -10.500 -22.500 -34.000
> SA surface: setting up working
> radii
> SA surface: found nonzero radii 3777
> Number of SA srf points exposed455488
> SA Bomb in sa_arc(): Allocation
> aborted 0 0 41
> 0 0
>
>
>
>
>
>
>
> Vikas Sharma (+91-9780449303)
> Molecular Modeling lab.
> Department of Medicinal Chemistry
> National Institute of Pharmaceutical Education & Research (NIPER),
> SAS Nagar, Mohali,
> Punjab (INDIA)
>
>
>
>
> ________________________________
> From: Ray Luo <ray.luo_at_uci.edu>
> To: AMBER Mailing List <amber_at_ambermd.org>
> Sent: Saturday, 6 June, 2009 8:07:43 PM
> Subject: Re: [AMBER] Error in MM PBSA
>
> Vikas,
>
> The error message is due to lack of memory on your computer. First set fillratio = 2 for proteins, and if the error message persists, increase space to 0.75, 1.00, and so on.
>
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Associate Professor
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900 Email: rluo_at_uci.edu
> Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
>
> Vikas Sharma wrote:
>
>> Dear Dr. Ray Luo,
>>
>> Sorry for replying so late...actualyy i checked the output file, found an erro..rectified it and re-ran the command:
>>
>> mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>>
>>
>> i got the follwing error:
>>
>> /opt/amber10/exe/sander -O -i pbsa_com.in -o pb sa_com.7.out -c /home/bharatam/amberresults_w/amberresults31/snapshot_com.crd.7 -p /home/bha ratam/amberresults_w/amb31/A31.prmtop not successful
>>
>> the contents of the output file are pasted below:
>> ======== Setting up Grid Parameters ========
>> Using bounding box for grid setup
>> Bounding Box Center: 47.000 43.500 29.000
>> Xmin, Xmax, Xmax-Xmin: -6.933 100.641 107.574
>> Ymin, Ymax, Ymax-Ymin: -18.558 105.341 123.899
>> Zmin, Zmax, Zmax-Zmin: -29.798 88.266 118.064
>> beginning box center at level 1 47.000 43.500 29.000
>> beginning box center at level 2 47.000 43.500 29.000
>> Grid dimension at level 1 109 125 119
>> Grid origin corrected at level 1 -173.000 -208.500 -211.000
>> Grid dimension at level 2 229 263 251
>> Grid origin corrected at level 2 -10.500 -22.500 -34.000
>> SA surface: setting up working radii
>> SA surface: found nonzero radii 3777
>> Number of SA srf points exposed455488
>> SA Bomb in sa_arc(): Allocation aborted 0 0 41
>> 0 0
>>
>>
>
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