Re: [AMBER] GDP and MG parameters

From: FyD <>
Date: Tue, 28 Aug 2012 18:17:17 +0200

Dear Vlad,

> Maybe I am blind here but I could not find GDP in the project F-90 or
> F-91 .. I also tried to search the RED database with "GDP" or "GTP" as
> molecule names but no results matched.
> Could you please point me more precisely how to efficiently search for GDP ?

GDP is constructed from molecular fragments...

See the abstract of F-90 & F-91:
- XYP (Adenosine monophosphate, Adenosine diphosphate, Adenosine
triphosphate, ...),
with X = 2'-Deoxyadenosine, 2'-Deoxycytidine, 2'-Deoxyguanosine,
2'-Deoxythymidine, Adenosine, Cytidine, Guanosine or Uridine, and Y =
any positive integer value

You go at:

-- R.E.DD.B. code (if known)
-- Molecule keyword *
-- Molecule name
-- Author lastname
-- Theory level/Basis set
          Text cofactor

Search... [Done]
Result(s) for search by Molecule keyword cofactor

Project name Cofactor_(biochemistry)
Project code F-90
Summary of information Click Here
Project name Cofactor_(biochemistry)
Project code F-91
Summary of information Click Here

In relation with:

Then, you go at:
You download the compressed archive:
You get all the files: tar jxvf F-90.tar.bz2 && cd F-90

Then, you run:
perl -p -i.old -e 's/\#\#\!\# //g' script1.ff
perl -p -i.old -e 's/\#\#\#\#\#\# //g' script1.ff
grep -v "to be replaced by the correct tripos" script1.ff > script1-new.ff
   (these commands are described in script1.ff from the extracted
project you downloaded or at
tleap -f script1-new.ff

You get mol2 files + mol3 files (concerning mol3 files see or download the
latest version of the AmberTools).

> P.S. Do you know any reference that used these parameters ?

I did not do a rigorous search about that.
I know this paper:

This additional web page might help you as well (but this is about the
R.E.D. tools):

I hope this helps.

regards, Francois

> On 08/28/2012 12:15 PM, FyD wrote:
>> Vlad,
>> You might look in R.E.DD.B.; See the F-90 & F-91 projects:
>> You will find many FF libraries for more than 200 cofactors; GMP, GDP,
>> GTP are obviously available...
>> regards, Francois
>>> I am looking into starting simulations of a protein that has a GDP and a
>>> MG ion in the active site.
>>> I know that in the database of AMBER parameters there are the Carlson
>>> parameters for GDP and the new Sorensen parameters for MG.
>>> I also found this comment from David Case which made me wonder about
>>> GDP. Is there anything new on the paper mentioned there ?
>>> I also read carefully this thread.
>>> Before starting simulations, I would be very grateful if people that
>>> have been using these parameter sets would comment on their experience
>>> with them (besides what is published in the respective references).
>>> If people are aware of other parameter sets, not available in the data
>>> base but worth trying out, I would also be very interested.
>>> Best wishes
>>> Vlad

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Received on Tue Aug 28 2012 - 09:30:03 PDT
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