Hi, Thanks. Is there something I can read to get more information as to how this is done?
Best, Irem > On Jun 2, 2016, at 1:06 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > Hi Irem, > > pdb2gmx checks the hydrogen bonding network and decides which form of His > fits best. > > Cheers, > > Tsjerk > On Jun 2, 2016 17:20, "Irem Altan" <irem.al...@duke.edu> wrote: > >> Hi, >> >> When I process a .pdb structure using pdb2gmx, how does Gromacs add >> hydrogens to the histidine residues? I see that in the processed structure, >> some histidines have their NE2 atom protonated, while some have ND1 >> protonated. How does Gromacs decide which nitrogen to protonate? >> >> Best, >> Irem >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=NeKtPfZmomO7TY28nP-DKDvbsgZ5lLg68UpgcmP1B_Y&e= >> before >> posting! >> >> * Can't post? Read >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=1re0r4wCl8tw_YjRBOs7agHtwsReTnobB68U_GgXnf4&e= >> >> >> * For (un)subscribe requests visit >> https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=s1JlpSKFO9QEGwEr2Ud8DphQ33LwK9vu_EXIy8iv3Ao&e= >> or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=NeKtPfZmomO7TY28nP-DKDvbsgZ5lLg68UpgcmP1B_Y&e= > before posting! > > * Can't post? Read > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=1re0r4wCl8tw_YjRBOs7agHtwsReTnobB68U_GgXnf4&e= > > > * For (un)subscribe requests visit > https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=s1JlpSKFO9QEGwEr2Ud8DphQ33LwK9vu_EXIy8iv3Ao&e= > or send a mail to gmx-users-requ...@gromacs.org. -- 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.
