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.uci.edu>
To: AMBER Mailing List <amber.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.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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Received on Mon Jun 08 2009 - 01:09:11 PDT
