Free Energy Calculation: State B has non-zero total charge: -1.000000

User discussions
1

GROMACS version:2021
GROMACS modification: No
Dear Gromacs Users
I am trying to calculate the free energy of mutating from Arginine to Histidine residue in a protein. I have prepared the system using pmx tools
http://pmx.mpibpc.mpg.de/janssen_tutorial_peptide/index.html
I have neutralized the system but during the grompp I get the following error:-

State B has non-zero total charge: -1.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.

Could you please suggest to me how should I set state B to zero charge without affecting charge of state A?

Thanks in advance.
Sadaf

2

I suspect that you used genion to neutralize a system with a positively charged arginine, then defined state B as uncharged histidine, causing the -1 total charge in state B. Use a doubly protonated histidine instead.

More generally, state A and state B are the two end states for free energy computation. These are defined in the topology file. For the lines describing atoms or bonds in the system, you have mandatory parameters corresponding to state A. (These are also the ones used for non-free energy simulation - in these runs, the system is always in state A). Additionally, you can specify a second set of parameters on the same line, that corresponds to state B. For instance here, some atoms 9 to 15 have a different charge in state B. Atom 7 and 8 have only state A defined - implicitly they will be identical in state B.

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
[...]
; residue   2 GLUL rtp GLUL q  0.0
     7        NH1      2   GLUL      N      3      -0.47     14.007
     8          H      2   GLUL     HN      3       0.31      1.008
     9        CT1      2   GLUL     CA      3        0.07000     12.011      CT1    0.07000     12.011    
    10        HB1      2   GLUL     HA      3        0.09000      1.008      HB1    0.09000      1.008    
    11       CT2A      2   GLUL     CB      4       -0.18000     12.011     CT2A   -0.18000     12.011    
    12        HA2      2   GLUL    HB1      4        0.09000      1.008      HA2    0.09000      1.008    
    13        HA2      2   GLUL    HB2      4        0.09000      1.008      HA2    0.09000      1.008    
    14        CT2      2   GLUL     CG      5       -0.28700     12.011      CT2   -0.20300     12.011    
    15        HA2      2   GLUL    HG1      5        0.09000      1.008      HA2    0.09000      1.008    
[...]