[gmx-users] protein-DNA simulation with Amber port

[Alaguraj Veluchamy]

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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