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

David van der Spoel spoel at xray.bmc.uu.se
Sun May 6 08:33:30 CEST 2007

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. 
please be more specific on the error you encounter.

> Previously, we run the pdb2gmx and the genbox programs solving notation
> errors. Finally .top and coordinate files are generated without
> (apparently) errors.
What do you mean with "solving notation 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.
This may seem confusing but is nevertheless correct. The extra 
information in the gromos files is optional (and you will not find it in 
the opls files for instance). This is (briefly) described in section 
5.6.1 of the manual:

"Parameters can be added to bonds, angles, dihedrals and impropers, 
these parameters override the standard parameters in the .itp files. 
This should only be used in special cases. Instead of parameters, a 
string can be added for each bonded interaction, this is used in
GROMOS96 .rtp files. These strings are copied to the topology file and 
can be replaced by force field parameters by the C-preprocessor in 
grompp using #define statements. "

> 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.
> b) Is the cause of the error these format differences?
> Thanks in advance
> Mario Campo and Griselda Corral
> Fac. de Cs. Exactas y Naturales
> UNLPam 
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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