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--- 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 <fyd.q4md-forcefieldtools.org> 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: http://q4md-forcefieldtools.org/REDDB/download.php -- 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: http://en.wikipedia.org/wiki/Cofactor_(biochemistry) Then, you go at: http://q4md-forcefieldtools.org/REDDB/Projects/F-90/ You download the compressed archive: http://q4md-forcefieldtools.org/REDDB/projects/F-90/F-90.tar.bz2 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 http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff) tleap -f script1-new.ff You get mol2 files + mol3 files (concerning mol3 files see http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php 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: http://www.sciencedirect.com/science/article/pii/S104784771100205X This additional web page might help you as well (but this is about the R.E.D. tools): http://q4md-forcefieldtools.org/RED/popup/citation.php 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: >> http://q4md-forcefieldtools.org/REDDB/Projects/F-90/ >> http://q4md-forcefieldtools.org/REDDB/Projects/F-90/script1.ff >> http://q4md-forcefieldtools.org/REDDB/Projects/F-90/script3.ff >> >> 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 ? >>> http://archive.ambermd.org/201112/0208.html >>> >>> I also read carefully this thread. >>> http://archive.ambermd.org/201205/0530.html >>> >>> 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 _____________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Aug 28 2012 - 12:00:04 PDT