Date: Wed, 21 May 2025 18:51:07 +0700
Dear AMBER community,
I prepared my protein + peptide + lipid membrane system using
packmol-memgen. The protein and the peptide are not supposed to share any
covalent bond. When visualizing the system on PyMOL, I found a strange,
very long bond (approx. 5 nm long) between two alpha carbons. One carbon
belongs to the first residue of the peptide. The other belongs to the last
residue of the protein.
I replicated the system preparation on tleap and got the same problem.
Furthermore, tleap renumbered the residues of the peptide to pick up from
the end of the protein. As if the tools believe the protein and the peptide
were one single piece of protein.
I also attached an image to this email so that you can have a look at the
problem.
Any help is appreciated.
Best regards,
-- *Lê Thanh Hòa (Mr.)* *Graduate student at International University, Vietnam National University * *Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
(image/png attachment: Selection_002.png)
