Hi Cheng, By default, the termini of a polypeptide are charged. You need option -noter
in your gmx pdb2gmx command to interactively tell it what charge (no charge in your case) you want for your termini. Best wishes, Dawid 2017-08-06 20:20 GMT+02:00 ZHANG Cheng <272699...@qq.com>: > Hi Mark, > Thank you. I have a glycine PDB: > > > ATOM 1 N GLY 3936 -1.908 -0.113 -0.081 1.00 20.00 > ATOM 2 CA GLY 3936 -0.753 0.774 0.097 1.00 20.00 > ATOM 3 C GLY 3936 0.558 0.024 0.014 1.00 20.00 > ATOM 4 O GLY 3936 0.474 -1.274 0.036 1.00 20.00 > ATOM 5 OXT GLY 3936 1.629 0.589 -0.066 1.00 20.00 > END > > > > Then, I use: > > > gmx pdb2gmx -f gly_clean.pdb -o gly_processed.gro -water spce > > > and got gly_processed.gro: > > > Glycine aRginine prOline Methionine Alanine Cystine Serine > 8 > 3936GLY N 1 -0.191 -0.011 -0.008 > 3936GLY H1 2 -0.275 0.042 -0.002 > 3936GLY H2 3 -0.186 -0.055 -0.098 > 3936GLY H3 4 -0.190 -0.081 0.063 > 3936GLY CA 5 -0.075 0.077 0.010 > 3936GLY C 6 0.056 0.002 0.001 > 3936GLY O1 7 0.047 -0.127 0.004 > 3936GLY O2 8 0.163 0.059 -0.007 > 0.43801 0.20480 0.16112 > > > > Can I ask, why there are still 3 hydrogens attached to the nitrogen? > > > Yours sincerely > Cheng > > > ------------------ Original ------------------ > From: "Mark Abraham";<mark.j.abra...@gmail.com>; > Date: Mon, Aug 7, 2017 01:48 AM > To: "gmx-users"<gmx-us...@gromacs.org>; "gromacs.org_gmx-users"<gromac > s.org_gmx-us...@maillist.sys.kth.se>; > Cc: "ZHANG Cheng"<272699...@qq.com>; > Subject: Re: [gmx-users] How to obtain a proper structure for glycine? > > > > > Hi, > > Prodrg is not gromacs software, so there is probably a better place to ask > this question. I'd also look at their docs to find out how to suggest a > carboxylic acid. > > Mark > > On Sun, 6 Aug 2017 18:09 ZHANG Cheng <272699...@qq.com> wrote: > > Dear Gromacs, > I would like to perform simulations for a protein with glycines. > > > I think I should use "insert-molecules" as shown on > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > gmx-tutorials/biphasic/01_genconf.html > > > So I went to PRODRG2 Server to obtain the glycine structure by "text > drawing": > > > O > " > N-C-C-O > > > But I got a suggested structure of NH3-CH2-COO, instead of NH2-CH2-COOH. > Can I ask why is that? > > > 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. > -- > 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. > -- 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.