Re: [gmx-users] How to obtain a proper structure for glycine?
Oh, I'm sorry for misleading you. You need use -ter The -noter means that you DON'T want to choose protonation yourself. Give this one a try. 2017-08-06 20:38 GMT+02:00 ZHANG Cheng <272699...@qq.com>: > Hi Dawid, > Thank you. However, I still got three hydrogens after running: > > > gmx pdb2gmx -f gly_clean.pdb -o gly_processed.gro -water spce -noter > > > gly_processed.gro: > > > Glycine aRginine prOline Methionine Alanine Cystine Serine10 3936GLY > N1 -0.191 -0.011 -0.008 3936GLY H12 -0.275 0.042 > -0.002 3936GLY H23 -0.186 -0.055 -0.098 3936GLY H34 > -0.190 -0.081 0.063 3936GLY CA5 -0.075 0.077 0.010 > 3936GLYHA16 -0.078 0.147 -0.062 3936GLYHA27 -0.083 > 0.121 0.099 3936GLY C8 0.056 0.002 0.001 3936GLY > O19 0.047 -0.127 0.004 3936GLY O2 10 0.163 0.059 > -0.0070.43801 0.27464 0.19713 > > > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Mon, Aug 7, 2017 02:20 AM > To: "Mark Abraham"; "gmx-users"< > gmx-us...@gromacs.org>; "gromacs.org_gmx-users" s.org_gmx-us...@maillist.sys.kth.se>; > > Subject: Re: [gmx-users] How to obtain a proper structure for glycine? > > > > 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 N1 -0.191 -0.011 -0.008 > 3936GLY H12 -0.275 0.042 -0.002 > 3936GLY H23 -0.186 -0.055 -0.098 > 3936GLY H34 -0.190 -0.081 0.063 > 3936GLY CA5 -0.075 0.077 0.010 > 3936GLY C6 0.056 0.002 0.001 > 3936GLY O17 0.047 -0.127 0.004 > 3936GLY O28 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";; > Date: Mon, Aug 7, 2017 01:48 AM > To: "gmx-users"; "gromacs.org_gmx-users" 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.
Re: [gmx-users] How to obtain a proper structure for glycine?
Hi Dawid, Thank you. However, I still got three hydrogens after running: gmx pdb2gmx -f gly_clean.pdb -o gly_processed.gro -water spce -noter gly_processed.gro: Glycine aRginine prOline Methionine Alanine Cystine Serine10 3936GLY N1 -0.191 -0.011 -0.008 3936GLY H12 -0.275 0.042 -0.002 3936GLY H23 -0.186 -0.055 -0.098 3936GLY H34 -0.190 -0.081 0.063 3936GLY CA5 -0.075 0.077 0.010 3936GLYHA1 6 -0.078 0.147 -0.062 3936GLYHA27 -0.083 0.121 0.099 3936GLY C8 0.056 0.002 0.001 3936GLY O19 0.047 -0.127 0.004 3936GLY O2 10 0.163 0.059 -0.0070.43801 0.27464 0.19713 -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 7, 2017 02:20 AM To: "Mark Abraham"; "gmx-users"; "gromacs.org_gmx-users"; Subject: Re: [gmx-users] How to obtain a proper structure for glycine? 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 N1 -0.191 -0.011 -0.008 3936GLY H12 -0.275 0.042 -0.002 3936GLY H23 -0.186 -0.055 -0.098 3936GLY H34 -0.190 -0.081 0.063 3936GLY CA5 -0.075 0.077 0.010 3936GLY C6 0.056 0.002 0.001 3936GLY O17 0.047 -0.127 0.004 3936GLY O28 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";; Date: Mon, Aug 7, 2017 01:48 AM To: "gmx-users"; "gromacs.org_gmx-users"; 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.
Re: [gmx-users] How to obtain a proper structure for glycine?
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 N1 -0.191 -0.011 -0.008 > 3936GLY H12 -0.275 0.042 -0.002 > 3936GLY H23 -0.186 -0.055 -0.098 > 3936GLY H34 -0.190 -0.081 0.063 > 3936GLY CA5 -0.075 0.077 0.010 > 3936GLY C6 0.056 0.002 0.001 > 3936GLY O17 0.047 -0.127 0.004 > 3936GLY O28 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";; > Date: Mon, Aug 7, 2017 01:48 AM > To: "gmx-users"; "gromacs.org_gmx-users" 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.
Re: [gmx-users] How to obtain a proper structure for glycine?
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 N1 -0.191 -0.011 -0.008 3936GLY H12 -0.275 0.042 -0.002 3936GLY H23 -0.186 -0.055 -0.098 3936GLY H34 -0.190 -0.081 0.063 3936GLY CA5 -0.075 0.077 0.010 3936GLY C6 0.056 0.002 0.001 3936GLY O17 0.047 -0.127 0.004 3936GLY O28 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";; Date: Mon, Aug 7, 2017 01:48 AM To: "gmx-users"; "gromacs.org_gmx-users"; 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.
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.
[gmx-users] How to obtain a proper structure for glycine?
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.
