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 -- 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].
