[gmx-users] Non integer charge for ARG and CYX?

[Georgios Patargias]

Hello 

Sorry if I address an already covered issue. I happened to notice that adding up 
the ffamber03 partial charges for ARG doesnt yield +1 but ~1.6. Also, for CYX
the total charge is ~0.87. Is this is a known issue? 

In the .itp file, pdb2gmx adds up rounded charge values (as seen in the qtot column)  
and so the total ARG charge comes up to +1 and for CYX 0. 

In .tpr, i.e. in the simulation, the full charge values are used, as they are contained in the 
ffamber03.rtp but grompp doesn issu warnings for non-integer total charge save for rounding 
errors. 

Thanks in advance. 

George



Dr. George Patargias
Polymer IRC Group
University of Leeds
Leeds, LS2 9JT, UK