[gmx-users] Document about file input format to GROMACS program?

[Mark Abraham]

root wrote:
> Dear GROMACS user:
> We downloaded the AMBER-03* potential parameters files
> (ffamber_v3.3.1-doc.tar.gz) linked with the page
> http://folding.stanford.edu/ffamber/index.html#validation. 
> We tried to simulate the Dickerson dodecamer using the 3.3.1 gromacs
> version.
> Our simulation crash when we run the grompp program. A (nonexistent)
> error in the atom numeration of the topology is indicated by the
> program.

Perhaps this is an English-usage issue, but I think your wording 
indicates an attitude where you think the problem is not being caused by 
fairly new users doing an unfamiliar task with well-tested and 
documented software, but by the authors of the software. What's more 
likely? :-) Moreover, if you want the latter to be keen to help you, 
then giving the impression you think it's their fault isn't a good way 
to go about it :-)

In particular, if you want help, you need to tell us grompp's diagnosis 
of the problem, not assert that there isn't one.

> Previously, we run the pdb2gmx and the genbox programs solving notation
> errors. Finally .top and coordinate files are generated without
> (apparently) errors.
> Analyzing the procedure, we observed that the format of the input files
> of the AMBER-03* potential (.rtp,.itp, etc.) frequently do not coincide
> with the input files included in the share/top folder of gromacs.
> For example the ffamber03.rtp file describe the bonds:
> ....
> [ bonds ]
>    H5T   O5'
>    O5'   C5'
>    C5'  H5'1
>    C5'  H5'2
>    C5'   C4'
>    C4'   H4'
> ....
> omitting the indication of the bond type, how for example occurs in
> ffG43a1.rtp
> .....
>  [ bonds ]
>     N     H    gb_2    
>     N    CA    gb_20   
>    CA     C    gb_26   
>     C     O    gb_4    
> .......
> The list of differences is long, and this is only one example.
> 
> The questions are:
> 
> a) There are any document indicating the format of the file inputs for
> the gromacs programs?
> The user manual 3.3 include little or not at all about this.

The whole of chapter 5 deals with this kind of issue, but only parts are 
relevant here. A good working knowledge of the contents of this chapter 
is essential to be effective when doing almost any non-trivial work with 
GROMACS.

> b) Is the cause of the error these format differences?

Mark