[gmx-users] on dummy atoms

[K.A. Feenstra]

David van der Spoel wrote:
> 
> On Fri, 11 Oct 2002, [gb2312] Áõ ËÉ°Ø wrote:
> 
> >hi, gang:
> >
> >I want to apply NMR distance restraints to a small molecular and I have
> >generated the topology file from PRODRG. But PRODRG only made ffgmx force
> >field topology file without full hydrogens, so I have to find a way to
> >get the position of hydrogens to be restrained and I don't want to bother
> >to build topology of the hydrogens. I think it may make sense to use
> >dummy atoms for applying restraints. I'm not sure about this. Does anyone
> >tell me something?
> It is not supported in the disres code, so you'll have to have the
> hydrogens explicitly. If you have a protein it is not a problem, otherwise
> you are on our own...
> You could specify dummy particles manually and have the disres work on
> that, but that seems tedious and error prone.

IIRC, dummy positions are generated before disre forces are calculated,
and dummy forces are distributed after disre forces are applied. So
it should work. Be sure to *Test* *It* *Thoroughly*!.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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