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 = 0 NPARM = 0 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 = 0 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 0 dihedrals
| Duplicated 0 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 - 06:07:15 PDT
