[gmx-users] on dummy atoms
David van der Spoel
spoel at xray.bmc.uu.se
Sat Oct 12 08:10:47 CEST 2002
On Fri, 11 Oct 2002, [gb2312] Áõ ËÉ°Ø wrote:
>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.
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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