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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
