Hi all,
I am getting an error while running minimization of my protein ligand
system.
I used ambertools 12 for preparing files and running sander on amber 9
i get following error in minout file:
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 09/15/2012 at 14:06:32
[-O]verwriting output
File Assignments:
| MDIN: complex-min.in
| MDOUT: complex-min.out
|INPCRD: complex-water.crd
| PARM: complex-water.top
|RESTRT: complex-min.rst
| REFC: complex-water.crd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
Initial minimisation of p38 MAPK anisomycin complex
&cntrl
imin=1, maxcyc=2500, ncyc=1000,
ntpr=5,ntr=1,restraint_wt=10,
cut=16, ntb=0, igb=1,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 09/15/12 Time = 14:48:33
NATOM = 51302 NTYPES = 16 NBONH = 48445 MBONA = 2921
NTHETH = 6483 MTHETA = 3967 NPHIH = 12725 MPHIA = 9165
NHPARM = 0 NPARM = 0 NNB = 92379 NRES = 15554
NBONA = 2921 NTHETA = 3967 NPHIA = 9165 NUMBND = 46
NUMANG = 100 NPTRA = 60 NATYP = 32 NPHB = 1
IFBOX = 1 NMXRS = 39 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 3489141
| Hollerith 323368
| Integer 1105924
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 32842 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
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 = 5, 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 = 1, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 16.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Energy minimization:
maxcyc = 2500, ncyc = 1000, ntmin = 1
dx0 = 0.01000, drms = 0.00010
Setting ifbox to 3 for non-orthogonal unit cell
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
defa
| INFO: Old style inpcrd file read
----- READING GROUP 1; TITLE:
rfree: End of file on unit 5
please help what could be the possible reason? is it because i am using two
different versions? but i am using anbertools 12 to create inpcrd file and
its saying "Old style inpcrd file read"
--
Jitesh V. Doshi
Research Associate,
Bioinformatics Centre,
University of Pune.
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Received on Sat Sep 15 2012 - 03:30:03 PDT
