[gmx-users] Document about file input format to GROMACS program?
Mark.Abraham at anu.edu.au
Sun May 6 19:20:05 CEST 2007
> Dear GROMACS user:
> We downloaded the AMBER-03* potential parameters files
> (ffamber_v3.3.1-doc.tar.gz) linked with the page
> We tried to simulate the Dickerson dodecamer using the 3.3.1 gromacs
> Our simulation crash when we run the grompp program. A (nonexistent)
> error in the atom numeration of the topology is indicated by the
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
> [ 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
> b) Is the cause of the error these format differences?
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