AMBER Archive (2009)

Subject: Re: [AMBER] Error in MM PBSA

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Sun Jun 07 2009 - 12:02:03 CDT


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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