AMBER Archive (2009)

Subject: [AMBER] large resp charges for non-natural amino acid

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Tue Jan 27 2009 - 16:40:49 CST

Hi,

I have performed 3 conformation RESP fitting to calculated charges for
alpha-carboxyl-glutamic acid. I have used as a basis AMBER advance
tutorial about fluorescein and linker (tutorial A1). What I did I capped
my residue with ACE and NME groups. Minimized 3 conformations.
Restrained cap charges as said in the tutorial.

Everything works fine, except CA gets charge 1.2 after RESP fitting.
Also other atoms in peptidic fragment have larger charges. Any
suggestion or comments ? To increase RESP restrain factor ? Increase
number of points in ESP calculations? Or maybe for amino acids (ff99SB)
there is another protocol to develop charges ?

best
Arturas 

-- 

Arturas Ziemys, PhD
  School of Health Information Sciences
  University of Texas Health Science Center at Houston
  7000 Fannin, Suit 880
  Houston, TX 77030
  Phone: (713) 500-3975
  Fax:   (713) 500-3929  

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