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

[TJ Piggot]

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 
<alaguraj_v at yahoo.com> 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
t.piggot at bristol.ac.uk
University of Bristol, UK.