AMBER Archive (2006)

Subject: AMBER: Problem working with Antechamber

From: nur avneet (
Date: Tue Oct 17 2006 - 02:44:54 CDT

Dear All
 I want to load peptoid Residues (peptoids have their side chain appended to amide nitrogen rather then alpha carbon) using antechamber.
 I have the pdb files, so i am using the command:
 $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2
 But I am facing two major problems:
 1) If i load single residues and then use leap to load the sequence, I fail and Leap window closes itself and the terminal displays error
 2) If i load the entire sequence of about 12 residues that include charged residues also (like lysine) then it says odd number of electrons (it does not consider the charge of the residues) and prepin file is not prepared.
 Please suggest how to proceed
 Avneet Saini
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