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 <[EMAIL PROTECTED]> 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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