[gmx-users] GTP topology file for ffG43a1

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 30 20:11:51 CET 2007

Quoting Robert Fenwick <rbf22 at mole.bio.cam.ac.uk>:

> Dear all,
> I have now prepared what I think are the necessary lines for entry
> into the ffG43a1.rtp file for GTP, however I was wanting a quick way
> to test what I have done. Again I am open to suggestions.
> Specifically I want to ensure that I have added sufficient bonds and
> angles for the molecule and that I have not defined any of the
> parameters more than once. I am quite happy to send on my files, if
> someone would like to help, basically my approach has been to
> cannibalise the ATP, AED and GUA files.
> Is there a simple way to produce a .gro or .pdb file from my altered
> ffG43a1.rtp?

I don't think you can make a structure from just an .rtp entry, but you could
always draw the molecule with PRODRG to get the structure file, and then make
adjust the atom names such that are the same as those in the .rtp, and proceed
from there.


> Cheers,
> Bryn
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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