Hi Ibrahaim,
I don't use xleap often for this, I usually use tleap, but something that
may be causing your issue is the lack of "TER" flags between the individual
monomers. Otherwise it may be read into xleap from the pdb as one
continuous chain of amino acids, which could explain your cyclic structure.
Hopefully that helps. If this is an xleap specific issue, someone else will
probably chime in.
All the best,
Clorice
On Wed, Feb 9, 2022 at 2:15 PM Ibrahim Said <saidibrahim569.gmail.com>
wrote:
> Dear Amber users
> I'm using Amber 16. When using xleap to create *.prmtop and *.rst7 for a
> protein in dimer form, xleap adds many extra dimers and forms cyclic
> structure. Please, can someone help me.
> Thanks
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Received on Wed Feb 09 2022 - 11:30:02 PST
