Re: Queries on patches, GDP-topology

From: Leonardo Trabuco (
Date: Mon Jul 24 2006 - 14:20:17 CDT


On Sat, Jul 22, 2006 at 06:06:15PM +0530, wrote:
> The molecular system I have considered is a GTPase bound to its GEF
> (Guanine exchange factor) along with GDP and mg2+ ion.
> [...]
> B. My other query is on GDP.
> Since the topology I use(top_all27_prot_na.inp) has described only ADP,
> I did some changes so as to mimic ADP for my GDP (since its chemical
> formula is very similar).
> I manually changed the GDP residue in the gdp.pdb to ADP (kindly note, I
> could not use pdbresidue alias to put GDP as ADP ).
> And included pdbaliases for ADP atom (Pls see my psfgen file above)
> Can anybody tell me what other changes have to be included. or Is
> there any chamm topology & parameter file that comprises of GDP or do
> any of you have other suggestions to handle this?!

It is very easy to create a topology for GDP based on ADP. I'm attaching
a topology file that contains a GDP residue. No new parameters are


Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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