[gmx-users] ion mutation in FEP

[SEMRAN İPEK]

Dear Users,

I have been trying to carry out FEP calculations for a long time for
mutation of
Glutamine to Aspartic acid using gromacs 4.5.5. Unfortunately, some
questions and problems arises during calculations.
Here is the question of mine.With glutamine, the
protein charge is -12. To neutralize the system, I added 12 Na+ ions. When I
mutate GLN to ASP, the charge in state_B is -13. After I run the grompp
command, the result says that my State_B topology has -13 charge since I am
not including mutation of ion.
How can I mutate 1 particular ion to ensure the neutrality of the
state_B. How should I exactly modify my topology file to include counter
ions
for state B.
I am including the part of the mutation in topology file at the end of the
e-mail.
If you could help me, I really appreciate for you time and help.

 Residue 221 GLN rtp GLN ; q 0.0
2083 N 221 GLN N 894 -0.31 14.0067 ; qtot -4.31
2084 H 221 GLN H 894 0.31 1.008 ; qtot -4
2085 CH1 221 GLN CA 895 0 13.019 ; qtot -4
2086 CH2 221 GLN CB 895 0 14.027 ; qtot -4
2087 CH2 221 GLN CG 895 0 14.027 DUM 0 14.027 ; qtot -4
2088 C 221 GLN CD 896 0.29 12.011 C 0.27 12.011 ; qtot -3.71
2089 O 221 GLN OE1 896 -0.45 15.9994 OM -0.635 15.9994 ; qtot -4.16

2090 NT 221 GLN NE2 896 -0.72 14.0067 OM -0.635 15.9994 ; qtot -4.88
2091 H 221 GLN HE21 896 0.44 1.008 DUM 0 1.008 ; qtot -4.44
2092 H 221 GLN HE22 896 0.44 1.008 DUM 0 1.008 ; qtot -4
2093 C 221 GLN C 897 0.45 12.011 ; qtot -3.55
2094 O 221 GLN O 897 -0.45 15.9994 ; qtot -4
**********************************************************************************


[ moleculetype ]
; Name nrexcl
NA+Mg 1

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 NA+ 20167 NA NA+ 1 1.0 22.9898 MG2+ 2.0 24.30 500


; Compound #mols
Protein_chain_C 1
FMT 1
SOL 19795
NA 12