I sent the same message already yesterday but it doesn't seem to have
come through. Sorry if it did, and it was just me who for whatever
reason didn't get it.
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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