Re: [gmx-users] How to adjust the default protonation states in martini itp files?
Dear Peter, Thank you very much! I will use GLU0 and -nt. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Tue, Jan 29, 2019 08:38 AM To: "gromacs.org_gmx-users"; Subject: How to adjust the default protonation states in martini itp files? 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: 1Qd 1 METBB 1 1. ; C 2C5 1 MET SC1 2 0. ; 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 SC12 0 should I change to this? 1P5 1 METBB 1 0. ; C 2C5 1 MET SC1 2 0. ; C 2) For side chains, e.g. GLU 362P5 165 GLUBB 362 0. ; C 363Qa 165 GLU SC1 363 -1. ; 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 GLU0BB 1 0 2 P1 1 GLU0SC12 0 should I change to this? 362P5 165 GLU0 BB 362 0. ; C 363P1 165 GLU0 SC1 363 0. ; 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to adjust the default protonation states in martini itp files?
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: >> 1Qd 1 METBB 1 1. ; C >> 2C5 1 MET SC1 2 0. ; 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 SC12 0 >> >> >> >> should I change to this? >> 1P5 1 METBB 1 0. ; C >> 2C5 1 MET SC1 2 0. ; C >> >> >> >> 2) For side chains, e.g. GLU >> 362P5 165 GLUBB 362 0. ; C >> 363Qa 165 GLU SC1 363 -1. ; 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 GLU0BB 1 0 >> 2 P1 1 GLU0SC12 0 >> >> >> >> should I change to this? >> 362P5 165 GLU0 BB 362 0. ; C >> 363P1 165 GLU0 SC1 363 0. ; 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to adjust the default protonation states in martini itp files?
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: > 1Qd 1 METBB 1 1. ; C > 2C5 1 MET SC1 2 0. ; 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 SC12 0 > > > > should I change to this? > 1P5 1 METBB 1 0. ; C > 2C5 1 MET SC1 2 0. ; C > > > > 2) For side chains, e.g. GLU > 362P5 165 GLUBB 362 0. ; C > 363Qa 165 GLU SC1 363 -1. ; 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 GLU0BB 1 0 > 2 P1 1 GLU0SC12 0 > > > > should I change to this? > 362P5 165 GLU0 BB 362 0. ; C > 363P1 165 GLU0 SC1 363 0. ; 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 gmx-users-requ...@gromacs.org.
[gmx-users] How to adjust the default protonation states in martini itp files?
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: 1Qd 1 METBB 1 1. ; C 2C5 1 MET SC1 2 0. ; 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 SC12 0 should I change to this? 1P5 1 METBB 1 0. ; C 2C5 1 MET SC1 2 0. ; C 2) For side chains, e.g. GLU 362P5 165 GLUBB 362 0. ; C 363Qa 165 GLU SC1 363 -1. ; 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 GLU0BB 1 0 2 P1 1 GLU0SC12 0 should I change to this? 362P5 165 GLU0 BB 362 0. ; C 363P1 165 GLU0 SC1 363 0. ; 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 gmx-users-requ...@gromacs.org.
