[gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

[parichita parichita]

Thaks for your suggesion... 
 
I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the 
problem I encounter is that the pdb2gmx produces the topologies where hydrogens 
sitting on carbons are condensed on carbon atoms they sit on. I need them explicitly 
since I would like to study the NMR coupling contanst of hydroxy protons and C-H protons.I 
mean 3J(H-O-C-H) and measure the distance between the C-H proton through the glycosidic linkage. 
So my questions are;

1- Are the force fields(45a3,53a5) that are implemented in Gromacs capable of taking care 
of hydrogens sitting on carbon atoms in a sugar molecule explicitly?

2- How can I most reliably produce topologies for my disaccharide that will 
be placed in a water box to perform MD?


I am quite new to MD methods therefore I apologize already now if I put 
forward something incoherent.

Thanks for the help,
 

Tsjerk Wassenaar <tsjerkw at gmail.com> wrote: Parichita,

My guess is you only thought to have 1-6 linkage, because the atoms
seemed so nicely involved in the .pdb file. But you'll have to define
a bond explicitly or it won't be there to break in the first place. I
think you need to read up on topologies, force fields and general
background about simulating molecular systems. Chapter 5 is a must. If
you continue on this path, note that sugar dihedrals, especially the
ones connecting the rings, are complex. Check out Roberto Lins' paper
on the 45a3 force field.

Tsjerk

On 9/17/07, Mark Abraham  wrote:
> parichita parichita wrote:
> > Hi again.....
> >   Thank you for your help....
> >  I found my MANA in the ffG53a5.rtp and i can prepare
> > the .gro and .top file from pdb2gmx.
> > Now , i am facing another problem after solvation of
> > my solute when i run the minimization the 1-6 linkage
> > was broken ......
> > please help me out ........
>
> "linkage was broken" doesn't help us help you. Please describe in detail
> what you observed and why you think it was wrong.
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Parichita Mazumder 
Junior Research Fellow 
C/O Dr. Chaitali Mukhopadhayay 
Department of Chemistry 
University of Calcutta 
92,A P C Road 
Kolkata-700009 
India.


       
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