Re: Queries on patches, GDP-topology

Date: Tue Jul 25 2006 - 03:16:20 CDT

Hi Leanardo,
thanks so much for forwarding the topology for GDP molecule.
Ramya Gamini

> Hi,
> 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
> necessary.
> Best,
> Leo
> --
> Leonardo Trabuco, Ph.D. candidate
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign

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