[gmx-users] Minimization question

[Florian Haberl]

hi,

On Friday 23 December 2005 13:36, Alan Dodd wrote:
> Bonds in GROMACS don't break or form, that requires QM
> calculations I think.  If the bond is broken at the
> end, that probably means it was never there to begin
> with - check your topology file.  Alternatively, it
> could just be set too long so it looks broken, again,
> check your topology file.

Do you have a dimer structure of your protein,
perhaps you have not set the chain identifier correct.

So with no special options pdb2gmx will the ends
and you will have a huge bond distance ... 

> --- tprakci at ttnet.net.tr wrote:
> 
> > Hi gmx-users,
> > I am performing minimizaiton on a co-factor. (FAD) I
> > set up the topology and run the process. No problem
> > for these. But at the end, the resultant structure
> > shows that 2 bonds are broken. These occurs
> > repeatedly and does not resolve with changing mdp
> > options. I also used LINCS to keep the bonds. 
> > In addition the rest of the molecule shows no
> > considerable improvement.I will be glad to hear any
> > contributions. Thanks.


> > 
> > Mustafa Toprakci
> >  
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greetings,

florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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