[gmx-users] Dummy Problem.

[Anthony Cruz]

Hi Mark:
Thank you for your interest. No, it does not work without the constraint.  the 
dummy atom still collapsing with the ND atom.  Also I try:
 [ constraint ]
 ;  ai  aj funct           b0 
ND      CON	  2	   0.064381

But grompp give me the following error:
Cleaning up constraints and constant bonded interactions with dummy particles
ERROR: Cannot have constraint (86-87) with dummy atom (87)
Fatal error: There were 1 dummy atoms involved in constraints

Also I try to put all the [ dummies2 ] and [ constraints ]  after the bonding 
information with the same result, the collapsing of the dummy atom.

What could be the problem???

Anthony


On Tuesday 06 February 2007 8:08 pm, Mark Abraham wrote:
> Anthony Cruz wrote:
> > Hi Users:
> >
> >
> > In my topology before all the bonded information I add the following
> > lines with the appropiate numbers:
> >
> >  [ dummies2 ]
> > ;Dummy      from       funct    a
> >   CON    ND    OE       1       0.064381
> >
> > [ constraint ]
> > ;  ai  aj funct           b0
> > ND      OE	2	   0.12032
> >
> > The problem is that the dummy colapse with the ND atom during the EM. 
> > What could be the problem?  I need to add the dummies2 section in my
> > topology if it is present in the residue topology and it is present in my
> > pdb???
>
> Does it work without the constraint?
>
> Mark
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