Dear Jorden
hi
Please find the content of fine pbsa_com.1.out . Thank you
-------------------------------------------------------
Amber 9 PBSA Scripps/UCSF 2006
-------------------------------------------------------
| Run on 08/14/2009 at 19:13:47
[-O]verwriting output
File Assignments:
| MDIN: pbsa.in
| MDOUT: pbsa_com.1.out
|INPCRD: ./snapshot_com.crd.1
| PARM: ./GNNQQNYMYRSB.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,
&end
&pb
epsin = 1.0, epsout = 80.0,
istrng = 0, radiopt = 0,
sprob = 1.4, space = 0.5,
maxitn = 1000, npopt = 1,
cavity_surften = 0.0072, cavity_offset = 0.00,
npbverb= 1
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 07/27/09 Time = 17:43:38
NATOM = 1103 NTYPES = 12 NBONH = 490 MBONA = 615
NTHETH = 1064 MTHETA = 828 NPHIH = 2382 MPHIA = 1873
NHPARM = 0 NPARM = 0 NNB = 5759 NRES = 71
NBONA = 615 NTHETA = 828 NPHIA = 1873 NUMBND = 30
NUMANG = 53 NPTRA = 29 NATYP = 23 NPHB = 0
IFBOX = 0 NMXRS = 33 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 40858
| Hollerith 6691
| Integer 74998
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 638 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 1, nmropt = 0
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: 608305 268029 608305
no. of atoms processed in PB initialization: 1103
NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI
1 GLY N N3 0.294300 0.786900 0.955900 1.550000 1.550000
2 GLY H1 H 0.164200 0.000000 0.000000 1.300000 1.300000
3 GLY H2 H 0.164200 0.000000 0.000000 1.300000 1.300000
4 GLY H3 H 0.164200 0.000000 0.000000 1.300000 1.300000
5 GLY CA CT -0.010000 0.169000 1.572200 1.700000 1.700000
6 GLY HA2 HP 0.089500 0.000000 0.000000 1.200000 1.200000
7 GLY HA3 HP 0.089500 0.000000 0.000000 1.200000 1.200000
8 GLY C C 0.616300 0.616300 0.069300 1.700000 1.700000
9 GLY O O -0.572200 -0.572200 0.044100 1.500000 1.500000
10 ASN N N -0.415700 -0.143800 0.591600 1.550000 1.550000
11 ASN H H 0.271900 0.000000 0.000000 1.300000 1.300000
12 ASN CA CT 0.014300 0.119100 0.527900 1.700000 1.700000
------------------------------------------------------------------------------------------------------
1103 MOL H28 ho 0.425230 0.425230 0.425230 1.200000 1.200000
total system charges (+/-) for PB 0.0000 180.9628 -180.9628
cavity_surften = 0.0072 cavity_offset = 0.0000
SAS Surface: surface dots generated: 366
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
On Fri, Aug 14, 2009 at 8:05 PM, Jordan Monnet<monnet.jordan.free.fr> wrote:
> Hello,
>
> What does pbsa_com.1.out say?
>
> --jordan
>
> * workalemahu berhanu (wgberhanu.gmail.com) wrote:
>> Dear Amber users
>>
>> I am not getting the results for mmpbsa calculation Calculate the
>> binding free energy. Can anyone help me?
>> I have
>> given both my input and output files.
>> This is my input
>> .GENERAL
>> PREFIX snapshot
>> PATH ./
>> COMPLEX 1
>> RECEPTOR 1
>> LIGAND 1
>> COMPT ./GNNQQNYMYRSB.prmtop
>> RECPT ./GNNQQNYSB.prmtop
>> LIGPT ./MYR.prmtop
>> GC 0
>> AS 0
>> DC 0
>> MM 1
>> GB 2
>> 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
>> This is my Out put
>> =>> Init data
>> Presuming executables of amber suite to be in /u0/z/zz217/USG/amber/9.0/exe
>>
>> =>> Reading input parameters
>> Found PREFIX => snapshot
>> Found PATH => ./
>> Found COMPLEX => 1
>> Found RECEPTOR => 1
>> Found LIGAND => 1
>> Found COMPT => ./GNNQQNYMYRSB.prmtop
>> Found RECPT => ./GNNQQNYSB.prmtop
>> Found LIGPT => ./MYR.prmtop
>> Found GC => 0
>> Found AS => 0
>> Found DC => 0
>> Found MM => 1
>> Found GB => 2
>> 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
>> 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
>> $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>> /u0/z/zz217/USG/amber/9.0/exe/pbsa -O -i pbsa.in -o
>> pbsa_com.1.out -c ./snapshot_com.crd.1 -p ./GNNQQNYMYRSB.prmtop not
>> successful
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
> }><(({*>
> __/
>
> Jordan MONNET
> Bachelor in Biology & Computer science
> University of Paris Diderot (Paris VII)
>
> http://monnet.jordan.free.fr/
>
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Received on Wed Aug 19 2009 - 22:34:40 PDT
