AMBER Archive (2004)

Subject: Re: AMBER: atom type CM

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Jan 16 2004 - 15:17:29 CST

> I'm curious about atom type CM. It is defined as "sp2 C pyrimidines in pos. 5
> & 6" in parm99.dat, but seems to have many parameters that don't apply to
> standard nucleic acids. I've heard that there used to be an atom type for
> isolated (non-conjugated) double bonds. Is that CM? If so, would CM still be
> appropriate for isolated double bonds or have the parameters been altered in
> order to better suit pyrimidines?

I'm not sure if it will help, but almost 10 years ago I prepared
an improved description (vs. the paper) of the Cornell et al.
atom types with Professor Kollman (due to my lack of knowledge
of chemistry :-).

The definition of CM at that point was:

  CM: sp2 carbon, more double bonded character than benzene.

I found the page thanks to the wayback machine,

  http://archive.org
  http://web.archive.org/web/20010711190924/www.amber.ucsf.edu/amber/ff94/types94.html

Bill Ross

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AMBER Atom Types (parm94.dat)
These are the basic atom types in the AMBER Cornell et al. 1995 force field, adapted from Table 1 of that paper.
Note that this is a purely all-atom force field.

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Sp3 Carbons:
CT: any sp3 (four explicit substituents).
Sp2 Carbons:
C : any sp2 carbonyl carbon
C*: sp2 aromatic carbon in a five-membered ring next to two carbons (e.g. C_gamma in tryptophan).
CA: any sp2 aromatic carbon and C_epsilon of Arg.
CB: sp2 aromatic at junction of five- and six-membered rings (e.g. C_delta in tryptophan and C4 and C5 in purines Ade & Gua).
CC: sp2 aromatic in a five-membered ring with one substituent and next to a nitrogen (e.g. C_gamma in histidine).
CK: sp2 aromatic in a five-membered ring, between two nitrogens and bonded to one explicit hydrogen (C8 in purines).
CM: sp2 carbon, more double bonded character than benzene.
CN: sp2 aromatic junction between five- and six-membered rings and bonded to C-R and N-R (e.g. C_epsilon in Trp).
CQ: sp2 in six-membered ring between two lone pair nitrogens (e.g. C2 in purines).
CR: sp2 aromatic in a five-membered ring between two nitrogens (e.g. C_epsilon in histidine).
CV: sp2 aromatic in a five-membered ring next to a carbon and a lone pair nitrogen (e.g. C_delta in His(delta)).
CW: sp2 aromatic in a five-membered ring next to a carbon and NH (e.g. C_delta in His(epsilon) and in Trp).
Sp3 Nitrogens:
N3: any sp3 (four substituents; e.g. lysine-Nzeta).
Sp2 Nitrogens:
N : sp2 in amides.
N*: sp2 in five- or six-membered ring with substituent (e.g. N9 in purines, N1 in pyrimidines).
N2: sp2 in amines (e.g. nucleic acids, Arg, and guanidium ions).
NA: sp2 in aromatic rings with attached hydrogen (e.g. Gua, Trp, protonated His).
NB: sp2 in five-membered ring with lone pair (e.g. N7 in purines).
NC: sp2 in six-membered ring with lone pair (e.g. N3 in purines).
Sp3 Oxygens:
OW: oxygen in TIP3P water model.
OH: alcohols, tyrosine, and protonated carboxylic acids.
OS: ethers and esters.
Sp2 Oxygens:
O : carbonyl.
O2: anionic acids (e.g. carboxyl and phosphate).
Miscellaneous heavy atoms
P : phosphorus in phosphate groups.
S : sulfurs in disulfide linkages.
SH: sulfur in cysteine.
LP: lone pairs.
Hydrogens:
H : attached to N.
HO: in alchohols and acids.
HW: in TIP3P water model.
HS: attached to sulfur.
HA: attached to aromatic carbon.
HC: attached to aliphatic carbon with no electron-withdrawing substituents.
H1: attached to aliphatic carbon with one electron-withdrawing substituent.
H2: attached to aliphatic carbon with two electron-withdrawing substituents.
H3: attached to aliphatic carbon with three electron-withdrawing substituents.
HP: attached to carbon directly bonded to formally positive atoms (e.g. C next to NH3+ of Lys).
H4: attached to aromatic carbon with one electronegative neighbor (e.g. C5 of Trp, C6 of Thy).
H5: attached to aromatic carbon with two electronegative neighbors (e.g. H8 of Ade and Gua and H2 of Ade).

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Last modified: Tue Nov 15 18:50:23 1994

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