[AMBER] Peptide with non-standard residues

From: Andreas Tosstorff <andreas.tosstorff.cup.uni-muenchen.de>
Date: Fri, 27 Jan 2017 12:03:36 +0100

Hi all,


I am trying to generate a peptide with three non standard residues: pGlu
(aka PCA) - His - Gly

I tried generating tha parameter files for PCA in antechamber and then
load it into leap.

Then I used the sequence command: sequence {PCA HIS CGLY}

Then I generated the peptide bond between PCA and HIS and removed the
resulting 2H and O.


I cannot save the parameter files of the resulting peptide, because
several bond, angle and torsion parameters are missing.


What's the best way to approach this? I could not find a tutorial where
this is described.


Kind regards,


Andreas 

-- 
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Fri Jan 27 2017 - 03:30:02 PST
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