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
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