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

[Tsjerk Wassenaar]

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 <Mark.Abraham at anu.edu.au> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>


-- 
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