[gmx-users] pdb2gmx - .top missing values

[Dallas Warren]

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?

>Atom names are simply labels; you can chose whatever you want.
>But the way you do it seems sensible. If you want automatic

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

>hydrogen addition (requires .hdb entries), you must name/number
>hydrogens systematically (described in the manual under 'Hydrogen
>database').

I picked that up from the manual and will be looking at that as I add 
further residues etc.

Thank you for your assistance.  It is much appreciated.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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