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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Received on Wed May 09 2012 - 00:00:03 PDT
