[gmx-users] DNA adduct simulation: grompp error

[TJ Piggot]

For the missing whitespace warning you need cpp = /lib/cpp -traditional in 
you .mdp file.

For the error you most likely do not have an #ifdef _FF_AMBER statement in 
you spc.itp file.

These have both been discussed on the list before so search there for more 
details and also the ffamber website:

http://chemistry.csulb.edu/ffamber/

As for your choice of forcefield (and parameterising your adduct) this has 
been discussed numerous times before (including recently) so again search 
the mailing list or the gromacs wiki.

Tom

--On Wednesday, February 20, 2008 16:09:32 +0100 Nathalie Geneste 
<n.geneste at ism.u-bordeaux1.fr> wrote:

> Dear users,
>
> I have some problems to launch a simulation with my molecular system
> including 2 strands DNA + benzo[a]pyrene adduct.
> After some trials with default gromacs force fields, I downloaded
> ffamber99.
>
> I have 2 problems:
>
> 1) my benzo[a]pyrene adduct is not recognized by ffamber99. Could you
> propose me a force field compatible with my system ?
>
> 2) If I ignore my adduct, we obtained with success my topolgy files but
> now I got the following error with grompp:
> ...
> checking input for internal consistency...
> calling /usr/bin/cpp...
> In file included from /usr/share/gromacs/top/ffamber99.itp:20,
>                  from 1AXV_mod4.top:11:
> /usr/share/gromacs/top/ffamber99bon.itp:518:22: warning: missing
> whitespace after the macro name
> /usr/share/gromacs/top/ffamber99bon.itp:520:22: warning: missing
> whitespace after the macro name
> /usr/share/gromacs/top/ffamber99bon.itp:521:22: warning: missing
> whitespace after the macro name
> /usr/share/gromacs/top/ffamber99bon.itp:524:21: warning: missing
> whitespace after the macro name
> /usr/share/gromacs/top/ffamber99bon.itp:535:19: warning: missing
> whitespace after the macro name
> 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 gromppEkqU9b
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: toppush.c, line: 1108
>
> Fatal error:
> [ file "/usr/share/gromacs/top/spc.itp", line 41 ]:
>              Atom index (1) in settles out of bounds (1-0)
> -------------------------------------------------------
>
> Does anybody has an explanation ?
>
> Regards,
> Nathalie
>
>
> --
>
> ******************
> Dr. N. GENESTE
> Groupe LPTC
> ISM - UMR 5255 CNRS
> Université Bordeaux I
> Phone.: 05 40 00 28 43
> Fax: 05 40 00 22 67
>
> ******************
> Nouvelle adresse:
> n.geneste at ism.u-bordeaux1.fr
> ******************
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.