[gmx-users] pdb2gmx - .top missing values

[K.A. Feenstra]

Dallas Warren wrote:
> 
> Erik,
> 
> >Did you add the bonds for the new rtp entry? And did you get
> > any error messages when running pdb2gmx?
> 
> No error messages.  It generates a .gro, .top and posre.itp file.
> 
> Here is a section from what I have added to the .rtp file:
[...snip...]
> So I have put in formation on the atom name, type of atom it is,
> charge on that atom, group of atoms for charge, and then
> which atoms are linked to which. 

So, what then is your problem? Do you get [bonds], [angles] etc
sections in your .top file? If so, are the parameters missing?
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...

> Is the numbering system on the
> atoms OK? e.g. C1, C2, O2, H2, C3 ... etc?

Atom names are simply labels; you can chose whatever you want.
But the way you do it seems sensible. If you want automatic
hydrogen addition (requires .hdb entries), you must name/number
hydrogens systematically (described in the manual under 'Hydrogen
database').

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
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