You need to put the atom types defined in ffamber under [ atoms ] as
replacement of original
1 amber99_54 1 SOL OW 1 -0.82 15.99940
2 amber99_55 1 SOL HW1 1 0.41 1.00800
3 amber99_55 1 SOL HW2 1 0.41 1.00800
It is good to embrace it with some C preprocessor so as to make SPC
still works for other force field,
#ifdef (_FF_AMBER99)
1 amber99_54 1 SOL OW 1 -0.82 15.99940
2 amber99_55 1 SOL HW1 1 0.41 1.00800
3 amber99_55 1 SOL HW2 1 0.41 1.00800
#else
1 OW 1 SOL OW 1 -0.82
2 HW 1 SOL HW1 1 0.41
3 HW 1 SOL HW2 1 0.41
#endif
TJ Piggot wrote:
Hi,
If i remember correctly i also got this error with spc (and spc/e) and
the ffamber port. However i was only playing around in testing
different water models and did not spend ages trying to fix this
problem because i use tip3p or tip4p for most of my runs.
So as to the error i am not sure, however if you try one of the tip*p
water models i think that you should not get this error (remember to
have #include
ffamber_tip*p in your .top file).
Sorry i can't be of more help
Tom
--On Friday, June 01, 2007 01:25:22 -0700 Alaguraj Veluchamy
<[EMAIL PROTECTED]> wrote:
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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----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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