AMBER Archive (2004)

Subject: AMBER: RESP charges for protein fragment

From: Tom Turner (
Date: Tue Feb 17 2004 - 10:20:15 CST

I am attempting to work through what I believe is a fairly well-trodden
path but have come a little unstuck with RESP charge-fitting so I hope
somebody can assist me...

I have a large protein which contains a non-standard residue (Asparagine
with a GlcNAc sugar attached). In order to prepare the protein for MD
simulations in Amber, I am attempting to calculate the charge
distribution of the non-standard residue then fit partial RESP charges.
  To do this I first capped the Asn+GlcNac fragment with an ACE and an
NME in xleap then ran a Gaussian03 energy calculation using the input

#hf/6-31g(d) geom=connectivity Pop=MK iop(6/33=2) iop(6/42=6)

I now have a .log output file that I need to feed into RESP to get my
partial charges. I have used antechamber to do this, but I am unsure
how to restrain the partial charges on the capping residues to the
standard values as given in the Cornell 1995 forcefield paper. So
essentially my question is: How do you calculate a RESP fit whilst
imposing fixed partial charge values for specific atoms? Can
antechamber do this?

Any help greatfully appreciated.

On a related note: Does anybody know if the 1995 RESP paper by Cieplak,
Cornell and Bayly [ J. Comp. Chem. 16 (11) 1357-1377 ] exists
electronically anywhere?

Many thanks,

Thomas E. Turner
Imperial College London.

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