[gmx-users] pdb2gmx - .top missing values

[Erik Lindahl]

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...

Cheers,

Erik