[AMBER] RDF analysis of glucose made by GLYCAM problem

From: Hoshin Kim <85hskim.gmail.com>
Date: Wed, 14 Jul 2010 10:10:30 +0900

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,


Hoshin kim.

Hoshin Kim
Visiting Scholar
Department of Chemical and Biomolecular Engineering
North Carolina State University
Raleigh, NC 27695
Phone: 919-986-9258
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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(image/jpeg attachment: RDF_result.jpg)

Received on Wed Jul 14 2010 - 07:30:05 PDT
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