AMBER: xleap question

From: Anna Díaz Cirac <>
Date: Fri, 14 Sep 2007 18:26:33 +0200

Dear Amber users,

i use xleap to create a cyclic peptide, and i use head and tail amino acids
to constructed it and with bond command i connect both extrems to get the
cyclic peptide. Then i minimizate the structure and get a good structure.
Using AMBPDB i get the pdb file, and finally take the pdb to xleap again to
obtain de structure solvated. But the problem is that, when i load the pdb i
have an error:

Added missing heavy atom : .R<CGLN 10> .A<OXT 18>
total atoms in file: 199
leap added 1 missing atom according to residue templates

Leap change my GLN to CGLN and put a OXT atom in the terminal Cterminal. I
tried to seleted it again, erase it, bond again and sovated it....but of
corse i had problems with the unperturbed charge.

There's any reason why this happends? What I'm doing is the best way to
obtain the cyclic? Others visual programs understand the connection of
extrem amino acid.

And why if i use desc name.residue.atom doesn't say double bond in C=0 of
amino acid? or the program knows the distance?

Thanks and best regards

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Received on Sun Sep 16 2007 - 06:07:37 PDT
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