On Sun, Feb 8, 2015 at 2:15 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Instead of “add”, try “combine”. A word of caution here, though: tleap is stupid when it comes to combining two units -- all it does is paste the two of them together. So the only way that ‘combine’ will work is if the starting coordinates for both units are compatible with each other (for instance, if both units came from the same PDB file, but split in two). Otherwise, tleap will put the guanidine molecule on top of whatever else happens to exist at those coordinates from unit ‘w’.
FYI, in such cases you could potentially use the coordinate
manipulation commands in cpptraj (translate, rotate, rms, etc) to get
rid of any bad clashes.
-Dan
>
> system = combine {w r}
>
> Then, ‘system’ will be the unit with the combined coordinates of both w and r.
>
> HTH,
> Jason
>
> [1] In case you were curious, the add command could *probably* be changed to “add w r.1” -- r.1 is the 1st residue of the ‘r’ unit (since ‘r’ has only one residue, it is also the entire unit). Although I would still advocate the use of “combine” instead, or, better yet, just use a PDB file that contains *both* the guanidine and the protein together and use that.
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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Received on Sun Feb 08 2015 - 16:00:03 PST
