Re: [AMBER] Modified residue separated in leap module

From: David Case <>
Date: Tue, 17 Jan 2017 08:53:56 -0500

On Tue, Jan 17, 2017, asdda asa wrote:
> I am dealing with DNA topoisomerase I (pdb id 1K4T) which contain modified
> residues TGP and PTR.
> When loading the protein into Leap, all is going well, but when saving it
> as new pdb file, the PTR residue was separated from the protein.

We need to see the exact commands you used. Generally, you should load a
*single* PDB file into leap that contains everything. LEaP doesn't change
coordinates (expect for a rigid translation to the center of the box in
periodic simulations). So if the PTR is in the correct place, in the input
file, it should be in the correct place in the output pdb file.
> So how to keep the PTR as original. I attached the two pdb files, one is
> original (from, the second one is saved using leap module.

Nothing was attached. But note (as above), we need both the input pdb file
and the exact commands you used.


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Received on Tue Jan 17 2017 - 06:00:05 PST
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