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

[Peter Kroon]

I got an answer :)

> The GLU0 is good indeed. For the termini, it depends on the secondary
structure. Coil is the most likely for a terminus, so P5 should be OK.
Note that there is a -nt option in martinize that sets neutral termini.

> Jonathan


Peter

On 29-01-19 10:44, Peter Kroon wrote:
> 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