[gmx-users] pdb2gmx - .top missing values

[K.A. Feenstra]

Dallas Warren wrote:
> 
> Anton,
> 
> Thank you for the replies.
> 
> Yes, I know about and have been using the PRODRG server program.
> 
> > So, what then is your problem? Do you get [bonds], [angles] etc
> > sections in your .top file? If so, are the parameters missing?
> 
> Yes, it specifies between which ones the bonds, angles etc are.
> 
> > If you don't specify parameters in your .rtp (it appears you
> > don't), then you don't get parameters in your .top explicitly.
> > In that case, parameters are taken from the [*_types] defenitions
> > in your ff*.itp files. Much of this is also described in the
> > manual...
> 
> Ahhh, OK.  Sorry I was under the impression that it inserted all of those values into the .top file.  So the software calls
> up the ff*bon.itp file as required for how the angels, bond constants etc should be?

Yes -- that is what grompp does, at least its mayor task.
It reads in all the [*_types] definitions from the *.top and *.itp
files specified, and uses those to fill in all the blanks in the
[bonds] [angles] etc. definitions. If you prefer, you could also
follow the groMOS conventions for bonded-interactions, where they
are indicated by independent labels and not by combinations of
atom types. Basically this employs the cpp pre-processing directives
-- the first action of grompp is to 'drag' all your .top and .itp
files through cpp. Look at some of the ffG43*.itp files for examples.

> That is good to know.  I just noticed that in the .rtp files
> supplied that some use on convention of letters and others
> numbers.

Yes -- these differences are mostly historic (and therefore 
completely illogical).

> Thank you for your assistance.  It is much appreciated.

You are most welcome.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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