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
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