[gmx-users] Creating topology with bonds over pbc

[Mark Abraham]

On 4/10/2011 6:25 PM, Wojciech Müller wrote:
> Hi all,
> Let's say I created a pdb of a B-DNA Double-Helix with amber tools. 
> Now I would like to have a topology in which the last residues are 
> bonded to the first. How can I do that expect of actually mess 
> together a topology file by self written scripts and/or handwork? 

I've never done anything like it, but I would guess that you can
* generate with AMBER tools an equivalent non-periodic structure with 
suitable termini (you need the ordering of the atoms belonging to 
non-terminal monomers to match the ordering of your structure above),
* use pdb2gmx on that,
* take the top file and remove the atoms for the termini, and the 
intra-termini bonds,
* create the head-to-tail [ bonds ] in the .top file, and
* match that with your structure above for grompp.
Sounds like about 15 minutes' work, if you already know the .top file 
format and how to use AMBER tools.

Mark

> Also if create helix strings without substituting the terminal 
> phosphate pdb2gmx doesn't seem to accept it.
> Thanks for any hints,
> W.Müller