Dear Gmx-users,
I have followed http://folding.stanford.edu/ffamber/ for porting amber in
Gromacs and i am trying to simulate protein-DNA complex. Preprocessing the
topology files gives error as below:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22#
checking input for internal consistency...
calling /lib/cpp -traditional...
processing topology...
Generated 2628 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2628 of the 2628 1-4 parameter combinations
Cleaning up temporary file gromppkzsTQq
Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]:
Atom index (1) in settles out of bounds (1-0)
I checked at the spc.itp file and found that the line 41 is:
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16333
and i am using em.mdp file:
;
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
cpp = /lib/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 100
;
; Energy minimizing stuff
;
emtol = 2000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
I tried the earlier post suggestion: that "include spc.itp " line must be
before the "[molecule] section", but still gives the same error as:
Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]:
Atom index (1) in settles out of bounds (1-0)
Thanks and regards
-Alaguraj.V
ALAGURAJ VELUCHAMY
c/o Dr.S.KRISHNASWAMY,
CENTRE OF EXCELLENCE IN BIOINFORMATICS,
MADURAI KAMARAJ UNIVERSITY,
MADURAI, TN.
Ph:09486148690
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