Dear all
I have added the new AMBER ion definitions from Joung and Cheatham to
my ffamber* force field files. Following the nomenclature these ions
have in AMBER, I use the same name for the atom name, the residue
name, and the molecule type, which includes the charge. E.g., I have
In ions.itp:
####
[ moleculetype ]
K+ 3
[ atoms ]
1 amber99_92 1 K+ K+ 1
1 39.10000
####
and correspondingly
In ffamber*nb.itp:
####
amber99_92 K+ 0.0000 0.0000 A 3.03796E-01 8.10369E-01
####
Now, when using
genion -pname K+ (or -pname "K+" or -pname 'K+')
I get ion entries in the gro file for "K+" residues containing "K"
atoms, rather than "K+" atoms.
Naively, I had assumed that the name defined with -pname is the
residue name (= molecule type) and that genion looks up the
corresponding atom name in ions.itp. This is obviously not the case...
Some playing around seems to suggest that the string supplied with -
pname is indeed used as the residue name. However, "+", "-", and any
preceding or following digits are then stripped to produce the atom
name. So, e.g., -pname Xyz3% gives "Xyz3%" for both residue and atom
names, whereas -pname Xyz-3 produces atoms named "Xyz".
Is this an undocumented (and rather annoying and unnecessary) feature
or a bug?
Cheers
Hans
.......................................................
Dr. Hans Martin Senn
Lord Kelvin/Adam Smith Research Fellow
E-mail: [EMAIL PROTECTED]
Direct line: +44 (0)141 330 6574
Fax: +44 (0)141 330 4888
Department of Chemistry
Joseph Black Building
University of Glasgow
Glasgow G12 8QQ
Scotland, UK
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