[gmx-users] How to adjust the default protonation states in martini itp files?

[ZHANG Cheng]

Dear martini friends,


By default, the "martinize.py" will 


1) for backbone atoms, positively charge the N-terminus (atom type Qd), and negatively charge the C-terminus (atom type Qa).


2) for side chain chargeable residues, always positively charge the LYS and ARG and negatively charge the ASP and GLU.


Now I want to change the protonation states based on a particular pH as determined by pdb2pqr server.


1) For backbones, if my N-terminus residue is MET:
    1    Qd     1   MET    BB     1  1.0000 ; C
    2    C5     1   MET   SC1     2  0.0000 ; C



based on "martini_v2.2P_aminoacids.itp" for MET:
;id type resnr residu atom cgnr   charge
 1   P5   1     MET     BB     1      0    
 2   C5   1     MET     SC1    2      0  



should I change to this?
    1    P5     1   MET    BB     1  0.0000 ; C
    2    C5     1   MET   SC1     2  0.0000 ; C



2) For side chains, e.g. GLU
362    P5   165   GLU    BB   362  0.0000 ; C
363    Qa   165   GLU   SC1   363 -1.0000 ; C



if I do not want GLU to be negatively charged,


based on "martini_v2.2P_aminoacids.itp" for GLU neutral form:
;id type resnr residu atom cgnr   charge
 1   P5     1     GLU0    BB     1      0    
 2   P1     1     GLU0    SC1    2      0 



should I change to this?
362    P5   165   GLU0   BB   362  0.0000 ; C
363    P1   165   GLU0  SC1   363  0.0000 ; C



Thank you!


Yours sincerely
Cheng