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

[Peter Kroon]

Hi Zhang,


I'm fairly sure GLU0 does what you want, but I'm not 100% sure on the
terminus. It'll probably do what you want, but I've forwarded your
question to the group to be sure.


Peter

On 29-01-19 01:38, ZHANG Cheng wrote:
> 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