Re: [AMBER] GDP and MG parameters

From: Vlad Cojocaru <>
Date: Tue, 28 Aug 2012 20:42:22 +0200

Thanks a lot Francois for this detailed explanation. I appreciate it a lot.

Dr. Vlad Cojocaru
Max Planck Institute Muenster
Roentgenstrasse 20,
48149 Muenster, Germany
Tel: +49-251-70365324
Sent from my mobile phone; Sorry for being short and for any errors
FyD <> wrote:
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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