[gmx-users] What's the best software to use: cut and past receptor and ligand

[David]

On Wed, 2005-05-25 at 16:39 -0400, Kai Zhuang wrote:
> Dear gmx-users list folks:
> 
> I'm trying to model a receptor and ligand system.  the receptor is
> really huge and the idea
> right now is to only model a part of the receptor (as in cut off the
> irrelavent domains and focus on the binding domain).   the receptor
> and ligands are in two seperate pdb files.
> 
> what's the softwares or some ways i can do the editing to put two into
> the same file close to eachother as well as deleting the part of the
> receptor tht's unwanted?
> i've tried text edit it and that ended horriblly because i can't
> manage the cordinates.
You can just go ahead and build the complete complex, then freeze part
of it and use energy exclusions to select groups that do not interact. 
> 
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 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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