Fwd: AMBER: MMPBSA error

From: jitrayut jitonnom <jitrayut.018.gmail.com>
Date: Tue, 13 Jun 2006 23:28:43 +0700

Dear *Heike*
I don't understand what do you mean "Is the pdb-File correct? " Did you mean
the format pdb file? or you maybe mean the number atoms in pdb is correct
according to the mmpbsa script. Please give me some more details.

Thanks in advance for your help

Best regards

Jitrayut


---------- Forwarded message ----------
From: Heike.Meiselbach.chemie.uni-erlangen.de <
Heike.Meiselbach.chemie.uni-erlangen.de>
Date: 13 .. 2006, 22:27 .
Subject: Re: AMBER: MMPBSA error
To: amber.scripps.edu

Hi,

check your structure with:
ambpdb -p ../dock71.top < ../01_GenerateSnapshots/enz_pep_pH7_com.crd.1 >
check_Complex.pdb

Is the pdb-File correct? If this is not the case, look in your generate
snapshot input file: If your simulation was carried out in water, you must
set the box information to yes. NTOTAL, the number of all atoms (with
water end counterions).
You must create a topology file from your complex without water and
counterions.

good luck,
Heike





> Dear amber users
>
> This is errors from mmpbsa. I generate three parameters files of LIG,REC
> and
> COM. My mdcrd file is an explicit md including water. To do the mmpbsa, I
> generate the snapshots from this parameters files for the first step but
> the
> second step that all trajectories were calculated, I found errors which
> show
> below. So, I don't understand where this errors happend.
>
> Please help me for this problems.
>
> Thanks
>
> Jitrayut
>
>
>
> [jitrayut.localhost 02_MMPBSA_Stability]$ /AMBER/amber9/exe/sander
> -O -i sander_com.in -o sander_com.1.out -c
> ../01_GenerateSnapshots/enz_pep_pH7_com.crd.1 -p ../dock71.top not
> successful
> [2]- Exit 25 mm_pbsa.pl mm_pbsa.in >mm_pbsa.log
>
>
>
>
> -------------------------------------------------------
> Amber 9 SANDER 2006
> -------------------------------------------------------
>
> | Run on 06/10/2006 at 18:27:42
> [-O]verwriting output
>
> File Assignments:
> | MDIN: sander_com.in
> | MDOUT: sander_com.1.out
> |INPCRD: ../01_GenerateSnapshots/enz_pep_pH7_com.crd.1
> | PARM: ../dock71.top
> |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 MM GB
>
> cntrl
> ntf = 1, ntb = 0, dielc = 1.0,
> idecomp= 0,
> igb = 2, saltcon= 0.00,
> offset = 0.09,
> intdiel= 1.0, extdiel= 80.0,
> gbsa = 0, surften= 1.0,
> cut = 999.0, nsnb = 99999,
> scnb = 2.0, scee = 1.2,
>
> imin = 1, maxcyc = 1, ncyc = 0,
> &end
>
>
--------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
--------------------------------------------------------------------------------
>
> | Flags:
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/28/06 Time = 19:45:26
> NATOM = 27939 NTYPES = 16 NBONH = 26195 MBONA = 1781
> NTHETH = 3825 MTHETA = 2437 NPHIH = 7403 MPHIA = 4752
> NHPARM = NPARM = NNB = 51578 NRES = 8402
> NBONA = 1781 NTHETA = 2437 NPHIA = 4752 NUMBND = 46
> NUMANG = 92 NPTRA = 42 NATYP = 31 NPHB = 1
> IFBOX = 1 NMXRS = 25 IFCAP = NEXTRA = 0
> NCOPY = 0
>
> Implicit solvent radii are modified Bondi radii (mbondi)
>
> | Memory Use Allocated
> | Real 1788610
> | Hollerith 176038
> | Integer 617374
> | Max Pairs 1
> | nblistReal 0
> | nblist Int 0
> | Total 17072 kbytes
> | Duplicated dihedrals
> | Duplicated dihedrals
>
> BOX TYPE: RECTILINEAR
>
>
>
> 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 = 2, nsnb =
> 99999
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
> saltcon = 0.00000, offset = 0.09000, gbalpha= 0.80000
> gbbeta = 0.00000, gbgamma = 2.90912, surften = 1.00000
> rdt = 0.00000, rgbmax = 25.00000
> alpb = 0
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Energy minimization:
> maxcyc = 1, ncyc = 0, ntmin = 1
> dx0 = 0.01000, drms = 0.00010
> Setting ifbox to 3 for non-orthogonal unit cell
> | INFO: Old style inpcrd file read
>
>
>
--------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
--------------------------------------------------------------------------------
>
>
> FATAL: NATOM mismatch in coord and topology files
>

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Received on Wed Jun 14 2006 - 06:07:16 PDT
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