Re: [gmx-users] Hydrogen bonds for particular residue during simulations.
On 1/22/18 5:58 AM, Seera Suryanarayana wrote: Dear gromacs users, I have done simulations of 20 residue length of peptide for 100ns. I want to find hydrogen bonds for residue GLU-7. The topology information for this residue as follow. ; residue 7 GLU rtp GLU q -1.0 121 opls_238 7GLU N 39 -0.514.0067 ; qtot 4.5 122 opls_241 7GLU H 390.3 1.008 ; qtot 4.8 123 opls_224B 7GLU CA 39 0.14 12.011 ; qtot 4.94 124 opls_140 7GLU HA 39 0.06 1.008 ; qtot 5 125 opls_136 7GLU CB 40 -0.12 12.011 ; qtot 4.88 126 opls_140 7GLUHB1 40 0.06 1.008 ; qtot 4.94 127 opls_140 7GLUHB2 40 0.06 1.008 ; qtot 5 128 opls_274 7GLU CG 41 -0.22 12.011 ; qtot 4.78 129 opls_140 7GLUHG1 41 0.06 1.008 ; qtot 4.84 130 opls_140 7GLUHG2 41 0.06 1.008 ; qtot 4.9 131 opls_271 7GLU CD 420.7 12.011 ; qtot 5.6 132 opls_272 7GLUOE1 42 -0.815.9994 ; qtot 4.8 133 opls_272 7GLUOE2 42 -0.815.9994 ; qtot 4 134 opls_235 7GLU C 430.5 12.011 ; qtot 4.5 135 opls_236 7GLU O 43 -0.515.9994 ; qtot 4 Kindly suggest me how to create index file for this residue. Have you tried looking at the examples provided by make_ndx? Type "help" at the prompt and it will show you how to use the program. It's very simple. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Hydrogen bonds
Thanks, I will try this option too. But now I would want to look at the particular hydrogen bonds between protein and ligand if these h bonds are present after the simulations. So, please let me know how can I interpret this data that I sent? --- On Saturday, 4 July 2015 11:49 AM, soumadwip ghosh soumadwipgh...@gmail.com wrote: Hi, the -hbn option in g_hbond in connection to your issue of determining the hydrogen bond lifetime or stability does not tell you much. What you should be looking at is running the g_hbond with -ac flag which gives you the lifetime and H-bond formation energy between two groups specified by you in the index file using either a predetermined or the default distance and angle cut-off. GROMACS obeys the Luzar and Chandler description of H-bond kinetics which considers the H-bonds labile and the lifetime of the same is calculated from the rate constants of H-bond breaking and re-forming. Cheers, Soumadwip -- 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] Hydrogen bonds
Hi, the -hbn option in g_hbond in connection to your issue of determining the hydrogen bond lifetime or stability does not tell you much. What you should be looking at is running the g_hbond with -ac flag which gives you the lifetime and H-bond formation energy between two groups specified by you in the index file using either a predetermined or the default distance and angle cut-off. GROMACS obeys the Luzar and Chandler description of H-bond kinetics which considers the H-bonds labile and the lifetime of the same is calculated from the rate constants of H-bond breaking and re-forming. Cheers, Soumadwip -- 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] Hydrogen bonds
On 7/4/15 3:05 AM, Dr. Seema Mishra wrote: Thanks, I will try this option too. But now I would want to look at the particular hydrogen bonds between protein and ligand if these h bonds are present after the simulations. So, please let me know how can I interpret this data that I sent? --- The index file produced by -hbn is meant to be used with the matrix produced by -hbm. This shows a time series of the breaking and forming of each individual hydrogen bond, as listed in the index file from -hbn. -Justin On Saturday, 4 July 2015 11:49 AM, soumadwip ghosh soumadwipgh...@gmail.com wrote: Hi, the -hbn option in g_hbond in connection to your issue of determining the hydrogen bond lifetime or stability does not tell you much. What you should be looking at is running the g_hbond with -ac flag which gives you the lifetime and H-bond formation energy between two groups specified by you in the index file using either a predetermined or the default distance and angle cut-off. GROMACS obeys the Luzar and Chandler description of H-bond kinetics which considers the H-bonds labile and the lifetime of the same is calculated from the rate constants of H-bond breaking and re-forming. Cheers, Soumadwip -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Hydrogen bonds
As a said the -hbn option in g_hbond is probably not informative in your case. First tell us what do you really want to observe? The no. of hydrogen bonds between specific amino acid residues and your ligand binding sites? If yes, use g_hbond with -num option that will give you the exact no of hydrogen bonds (second column of the num.xvg output file) and if you want to perform a kinetic analysis of hydrogen bond formation use the -ac flag. From the part of the file you sent in the previous mail I can not understand what exactly you want to achieve from g_hbond. Cheers, Soumadwip -- 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] Hydrogen bonds between new residue and protein.
I found one problem. If I create new group in index.ndx file which contains protein without CH6 residue then some h-bonds are detected but actually I wouldn't expect it the way it looks. So again, how does actually g_hbond calculate hydrogen bonds except the distance and angle restraints. Does it recognize donors and acceptors by the atom types? If so, how can I force it to recognize MO3 as h-bond acceptor for instance? 2014-08-20 16:44 GMT+01:00 Dawid das add...@googlemail.com: Dear Gromacs experts, This time I would like to use g_hbond to calculate hydrogen bonds between one residue of the protein and all other residues in the protein. The thing is that the former residue is a new one, defined by me from scratch. Now when I run g_hbond and choose CH6 and Protein index groups (CH6 is my new residue and Protein also includes this CH6 residue) I got 0.0 for every time step although I strongly believe there are couple of hydrogen bonds. I was thinking that the issue may be that CH6 is built of atomtypes which are not recognised by g_hbond as ones able to form hydrogen bonds. Is it possible explanation? If yes, what can I do? Is recompiling what I need to do? Thanks, Dawid Grabarek -- 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] Hydrogen bonds between new residue and protein.
On 8/20/14, 12:02 PM, Dawid das wrote: I found one problem. If I create new group in index.ndx file which contains protein without CH6 residue then some h-bonds are detected but actually I wouldn't expect it the way it looks. So again, how does actually g_hbond calculate hydrogen bonds except the distance and angle restraints. Does it recognize donors and acceptors by the atom types? If so, how can I force it to recognize MO3 as h-bond acceptor for instance? It reads the first character of atom names, nothing more. The best bet is to name atoms more conventionally, such that the first letter is the actual elemental symbol. You can do this after the simulation by editing the .top and producing a new .tpr file with new names. It doesn't affect the simulation in any way. -Justin 2014-08-20 16:44 GMT+01:00 Dawid das add...@googlemail.com: Dear Gromacs experts, This time I would like to use g_hbond to calculate hydrogen bonds between one residue of the protein and all other residues in the protein. The thing is that the former residue is a new one, defined by me from scratch. Now when I run g_hbond and choose CH6 and Protein index groups (CH6 is my new residue and Protein also includes this CH6 residue) I got 0.0 for every time step although I strongly believe there are couple of hydrogen bonds. I was thinking that the issue may be that CH6 is built of atomtypes which are not recognised by g_hbond as ones able to form hydrogen bonds. Is it possible explanation? If yes, what can I do? Is recompiling what I need to do? Thanks, Dawid Grabarek -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Hydrogen bonds
Hi, You need to inspect the -hbm and -hbn output. It's the complete existence matrix for all h-bonds encountered in the analysis and a list of corresponding acceptor-H-donor triads. Consequently those files are usually rather big, but that's where the information is. Inspect the bonds you find in pymol or whatever viewer you prefer though, for a common mistake is to read the matrix 'upside down'. Kind regards, Erik On 28 May 2014, at 05:59, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I want to find the interacting hydrogen bonding residues with the residue of my choice. I made an index for the residue for which I want to find the hydrogen bonds and I get the number of hydrogen bond it makes during the simulation. But how can I find the residue with which its making the hydrogen bonds. Regards -- Bharat -- 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] Hydrogen bonds
On 5/28/14, 12:59 AM, bharat gupta wrote: Hi, I want to find the interacting hydrogen bonding residues with the residue of my choice. I made an index for the residue for which I want to find the hydrogen bonds and I get the number of hydrogen bond it makes during the simulation. But how can I find the residue with which its making the hydrogen bonds. Obtain the existence map and corresponding index file that labels which H-bond is which using -hbn -hbm. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
