[gmx-users] on dummy atoms

[David van der Spoel]

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.


Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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