AMBER Archive (2005)

Subject: AMBER: (no subject)

From: ping jiang (p_jiang2000_at_yahoo.com)
Date: Fri Dec 23 2005 - 14:46:58 CST

Hi, all,

I am a new beginner of Amber package (Amber8), I have
some difficulties to assign the charges in general
organic molecules.
 
I want to build Sodium undecyl L-alanine Leucine. I
can draw the undecyl part in Xleap, then add to the
sequence of Ala & Leu, but there is no charge for the
atom in the undecyl part. I used Antechamer to
generate the undecyl-Ala-Leu with -1 charge to get the
atomtype and charge. I found the whole system had -1
charge, but the atoms in the undecyl still no charge.
I am just wondering how to assign the charge in Amber
if you build some general organic molecules; I can
build the big molecules that I want to use in other
software, for example Sparton, but when I saved as
PDB, or Mol2..., it cannot be recognized by Amber. In
the tutorial, they have prepared the PDB file for the
molecule, which software do you use to get these PDB
files?
Any susgestion and help are appreciated!
Thanks
Ping

     
   
   
   
   
   
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