AMBER Archive (2006)

Subject: Re: AMBER: MMPBSA error

From: Heike.Meiselbach_at_chemie.uni-erlangen.de
Date: Tue Jun 13 2006 - 10:27:22 CDT

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_at_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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