Re: [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis
On 5/5/20 12:12 PM, Neena Susan Eappen wrote: Thank you Sahil, I will try VMD plugin for H-bond analysis. Thank you Justin for your reply, it looks like gmx hbond considers only one N-H as donor when part of NH2 group. Please take a look at this file. This is what gmx hbond does by default, see gmx help hbond: -[no]merge (yes) H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF. This is a very different situation than claiming the NH2 group simply isn't accounted for. -Justin https://drive.google.com/file/d/1EgJPbHXNCo--VFOoy1YYolBx3XKBKpiH/view?usp=sharing Many thanks, Neena From: Neena Susan Eappen Sent: Tuesday, April 28, 2020 1:50 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx users] Terminal amide hydrogens not included in H-bond analysis Hello gromacs users, My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here? Many thanks, Neena -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] [gmx users] Terminal amide hydrogens not included in H-bond analysis
Thank you Sahil, I will try VMD plugin for H-bond analysis. Thank you Justin for your reply, it looks like gmx hbond considers only one N-H as donor when part of NH2 group. Please take a look at this file. https://drive.google.com/file/d/1EgJPbHXNCo--VFOoy1YYolBx3XKBKpiH/view?usp=sharing Many thanks, Neena From: Neena Susan Eappen Sent: Tuesday, April 28, 2020 1:50 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx users] Terminal amide hydrogens not included in H-bond analysis Hello gromacs users, My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here? Many thanks, Neena -- 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] [gmx users] Terminal amide hydrogens not included in H-bond analysis
On 4/27/20 9:50 PM, Neena Susan Eappen wrote: Hello gromacs users, My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here? How do you know this group isn't being factored into the analysis? The NH2 residue is recognized as a protein residue by default and the analysis should consider all N-H pairs as H-bond donors. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] [gmx users] Terminal amide hydrogens not included in H-bond analysis
Hello, Though I don't know the answer to your question, I can offer a workaround for the task. I have simulated such C-terminally amidated peptides in vacuum before and I performed the same analysis using the Hydrogen bonds plugin in VMD. Hope this helps. Cheers, Sahil On 2020-04-28 07:20, Neena Susan Eappen wrote: > Hello gromacs users, > > My peptide has an amide group at the C-terminus. Hydrogen bond analysis using > gmx hbond does not take into account H-bond donors (NH2) from the amide group > (Note: this NH2 is considered as a residue according to opls ff). What might > be happening here? > > Many thanks, > Neena -- 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.
