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
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