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

[Hans Martin Senn]

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: 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