AMBER Archive (2003)

Subject: AMBER: Lone pairs and resp

From: Perdita Barran (perdita.barran_at_ed.ac.uk)
Date: Mon Nov 17 2003 - 10:49:35 CST

Dear Amber

We are trying to use the new force field ff02EP to model hydrogen
bonding
interactions of polypeptides in the gas-phase. The libraries associated
with
this force field: all_amino02EP.lib etc. seem to be defined such that
lone
pairs only exist for carbonyl oxygens (not for hydroxyl oxygens, not for

nitrogens and not even for 'free' acid COO- C-termini). Is there any
basis for
the fact that only carbonyl oxygens have lone pairs in ff02EP?

We would like to make new residues that reflect gas-phase protonation
sites,
based on existing residues in LeAP. For example we have made residues
for several amino acids with neutral termini and are now in the process
of remaking these according to the procedure from the paper that
describes the ff02EP force
field (P. Cieplak, J. Caldwell, P. Kollman, J. Comput. Chem., 2001, 22
(10),
1048-1057.) This utilises Gaussian B3LYP/cc-pVTZ to do an electrostatic
charge fitting
(ESP) and then uses the RESP (restrained electrostatic charge fitting)
procedure in antechamber to annotate the charges.

What is not clear in this procedure is where the lone pairs are
introduced. Are
dummy atoms made for the lone pairs before carrying out the ESP
procedure in
Gaussian? Or is the Gaussian output file modified to include the lone
pairs? Or
is the RESP procedure carried out once without the lone pairs to make a
prepi
file and this prepi file is then modified to include the lone pairs;
this is
followed by another RESP procedure.

Further, how does one declare the lone pair charge points in the RESP
procedure? These are defined as 'EP' in the LeAP libraries (e.g.
all_amino02EP.lib), but this annotation is not recognised by
antechamber. (Does
this mean that one uses 'DU' as a dummy atom instead of 'EP').

Thanks very much for your help. 

-- 
Nick Polfer
School of Chemistry
West Mains Road
Edinburgh EH9 3JJ
United Kingdom
++44 131 650 4773
++44 131 651 3048 (fax)

--------------------------------------------
Dr. Perdita Barran
EPSRC Advanced Research Fellow
School of Chemistry
The University of Edinburgh
Joseph Black Building
The King's Buildings
West Mains Road
Edinburgh EH9 3JJ

t: +44 (0) 131 650 7533 (office)
t: +44 (0) 131 651 3039 (lab)
f: +44 (0) 131 650 7533
e: perdita.barran_at_ed.ac.uk 
w: http://www.chem.ed.ac.uk/staff/barran.html

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