That someone was me. The "two residues" reference is to our
convention of splitting off the anomeric OH to facilitate building
branches. That is, a-D-Glcp is built with something like "sequence {
ROH 0GA }".
Hoshin Kim,
You say you are using 8 glucose molecules with waters. How are you
generating that file? There are many things that can go wrong.
Chances are that ptraj is working just fine and that your system
really is structured like that. If that is the case, we need to find
out why your system has that structure.
I assume from the implied use of a coordinate file (md_center.x) that
you ran an md. Have you visualized the trajectory using VMD? Doing
that will often explain many issues.
:-) Lachele
On Tue, Jul 13, 2010 at 9:10 PM, Hoshin Kim <85hskim.gmail.com> wrote:
> Dear Amber specialists,
>
> I'm trying to do simulation of solvation of glucose in water. And I tried to
> run PTRAJ to calculate RDF between glucose - glucose after 4.5ns MD run
> But there was a problem. First 2 peaks are too close. I think separated
> glucose molecule is the one of the main reason. Because when I made the
> glucose structure at GLYCAM website(structure builder), program made them
> with 2 residues even though glucose is monomer.
> My PTRAJ analysis input file is as follows,
>
> trajin md_center.x (already centered file was used)
> radial rdf_Glcglc 0.05 15.0 :1-16 :1-16 (I used 8 glucose molecule, but I
> defined 1-16 because of 2 residues of single glucose)
> radial rdf_glcwat 0.05 15.0 :WAT.O :1-16
>
> And attached file is the result of RDF by PTRAJ in AMBER 9 package, and
> XMGrace was used as plotting program
>
> I already sent GLYCAM developer an E_mail, they said sugar molecule composed
> of 2 residues is no problem to calculate RDF. They also said that "The
> division of molecules into convenient residues is a very common practice,
> particularly with oligomeric molecules. most software packages expect
> multiple residues per molecule.
>
> Are there someone who went through like me ? please give me an advice to
> solve this problem.
>
> Thanks in advance,
>
> Regards,
>
> Hoshin kim.
>
> ----------------------------------------------------------------------------
> -------
> Hoshin Kim
> Now)
> Visiting Scholar
> Department of Chemical and Biomolecular Engineering
> North Carolina State University
> Raleigh, NC 27695
> Phone: 919-986-9258
> Also)
> Graduate student (M.D. candidate)
> Ionic Liquids Team(ILs) in Bio Nano Process Lab
> Department of Biological Engineering,
> 2S 113, Engineering building Inha University,
> 253 Yonghyeon Dong, Nam Ku
> Incheon, KOREA
> TEL) +82-32-860-8655
> ----------------------------------------------------------------------------
> -------
>
>
>
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>
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Jul 14 2010 - 08:00:06 PDT
