[gmx-users] genion strips +, -, digits. Bug or feature?

[Hans Martin Senn]

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: senn at chem.gla.ac.uk
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