[gmx-users] pdb2gmx - .top missing values

[K.A. Feenstra]

Erik Lindahl wrote:
> 
> Dallas Warren wrote:
> 
> > I have been working on adding my own residue to .rtp, with all the
> > ffgmx* files copied to a new force field.
> >
> > I managed now to get pdb2gmx to process a pdb file containing the
> > residue and spit out the .gro and .top files.  However, the .top file
> > does not have the bond etc information in it.  Any suggestions on why
> > this might be the case?
> 
> Hi Dallas,
> 
> Did you add the bonds for the new rtp entry? And did you get any error
> messages when running pdb2gmx?
> 
> By the way - there's a program called x2top that can create rtp entries
> from coordinates...

And then there is Daan's PRODRG server which does similar things.
(Search this list for the adress, I don't know it.)


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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