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

David spoel at xray.bmc.uu.se
Wed May 25 23:14:58 CEST 2005

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 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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