[gmx-users] AMBER ff99SB port problems

[jantonioms J. A. Mondragon S]

I used amber ff99 port with ffamber_tip3p.tip and it's works fine. I changed
this in my molecule topology file. Up to now, nobody can say me why using
tip3p with amber ports doesn't work.

On Dec 7, 2007 11:57 AM, Shozeb Haider <shozeb.haider at pharmacy.ac.uk> wrote:

> Hi,
>
> I was wondering if any has expertise in using Amber ff99SB port (Pande's
> lab). I am currently using port for 3.3.1 version of gromacs.
>
> When I solvate my protein and run grompp to generate a tpr file, it
> gives me the following error
>
> 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 gromppXORFn5
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> 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)
> -------------------------------------------------------
>
>  From what it seems that the program is unable to communicate with
> spc.itp file. However that should not be the case since the program
> routinely does that when I run using other gromacs force fields. I have
> also explicitly included the /share/gromacs/top direcly as well
>
> I have the following lines in my preprocessor :
> cpp                 =  /lib/cpp -traditional  ; prepocessor of the
> current machine
> include             =  -I/usr/share/gromacs/top
> define              =
>
> Any suggestions would be much appreciated.
>
> Many thanks
>
> Shozeb Haider
> The London School of Pharmacy
>
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