[gmx-users] PROTEIN FOLDING
Hi gromacs users, After MD simulation of protein-ligand complex for 5ns, can we view protein folding? How to do it? I want to ascertain if there is any conformation change in protein where the ligand binds. Is it possible? We observe hydrogen bonds through molecular docking. Hence, I want to make observation through MD simulation which is not obtained through docking. Can someone help me regarding this? Thank you very much in advance. Thanks, Neha -- 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] PROTEIN FOLDING
Hi gromacs users, I have run 2ns simulation of protein ligand complex using NVT ensemble (after equilibration). I want to know whether there is a structural/conformational change in the protein especially in the active site where, the ligand forms hydrogen bonds with the protein during simulation. Can we visualize it? Is it possible? Please let me know. Thanks, Neha -- 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] PROTEIN FOLDING
After MD simulation of protein-ligand complex for 5ns, can we view protein folding? mostly, NO Search what time range 'protein folding' is happening. How to do it? I want to ascertain if there is any conformation change in protein where the ligand binds. Is it possible? You might want to do PCA, RMSD and DSSP We observe hydrogen bonds through molecular docking. Hence, I want to make observation through MD simulation which is not obtained through docking. gmx hbond Can someone help me regarding this? i really wondering what is possible in 5 ns simulation time, you may try to extend it up to 100 ns or atleast a 50 ns. Thank you very much in advance. -- 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] PROTEIN FOLDING
On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta wrote: > Hi gromacs users, > > After MD simulation of protein-ligand complex for 5ns, can we view protein > folding? You can use various supporting tools from R language to debug your trajectory but most third party software support NAMD and charmm format. You can use VMD to convert the trajectory to dcd and use R language based packages to read your trajectory > > > How to do it? > > I want to ascertain if there is any conformation change in protein where > the ligand binds. Is it possible? > > We observe hydrogen bonds through molecular docking. Hence, I want to make > observation through MD simulation which is not obtained through docking. > > Can someone help me regarding this? > > Thank you very much in advance. > > Thanks, > Neha > -- > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] PROTEIN FOLDING
On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta wrote: > Hi gromacs users, > > After MD simulation of protein-ligand complex for 5ns, can we view protein > folding? > > How to do it? > > I want to ascertain if there is any conformation change in protein where > the ligand binds. Is it possible? > > We observe hydrogen bonds through molecular docking. Hence, I want to make > observation through MD simulation which is not obtained through docking. You can perform Clustering analysis over particular PC sub space to measure the structural changes. > > > Can someone help me regarding this? > > Thank you very much in advance. > > Thanks, > Neha > -- > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] PROTEIN FOLDING
Hi, Thank you for your prompt reply. By clustering analysis, are you talking about gmx cluster command? "over particular PC sub space" Could you please elaborate a bit? Thanks a lot once again. Thanks, Neha On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH wrote: > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > wrote: > > > Hi gromacs users, > > > > After MD simulation of protein-ligand complex for 5ns, can we view > protein > > folding? > > > > How to do it? > > > > I want to ascertain if there is any conformation change in protein where > > the ligand binds. Is it possible? > > > > We observe hydrogen bonds through molecular docking. Hence, I want to > make > > observation through MD simulation which is not obtained through docking. > > > You can perform Clustering analysis over particular PC sub space to measure > the structural changes. > > > > > > > Can someone help me regarding this? > > > > Thank you very much in advance. > > > > Thanks, > > Neha > > -- > > 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. > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > 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] PROTEIN FOLDING
On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta wrote: > Hi, > > > Thank you for your prompt reply. > > By clustering analysis, are you talking about gmx cluster command? > > "over particular PC sub space" > > Could you please elaborate a bit? Yea clustering analysis can interpret a lot datas about your complex simulation. Note: I am not sure whether you Can perform gmx cluster over particular sub space. > > > Thanks a lot once again. > > Thanks, > Neha > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH > wrote: > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > > wrote: > > > > > Hi gromacs users, > > > > > > After MD simulation of protein-ligand complex for 5ns, can we view > > protein > > > folding? > > > > > > How to do it? > > > > > > I want to ascertain if there is any conformation change in protein > where > > > the ligand binds. Is it possible? > > > > > > We observe hydrogen bonds through molecular docking. Hence, I want to > > make > > > observation through MD simulation which is not obtained through > docking. > > > > > > You can perform Clustering analysis over particular PC sub space to > measure > > the structural changes. > > > > > > > > > > > Can someone help me regarding this? > > > > > > Thank you very much in advance. > > > > > > Thanks, > > > Neha > > > -- > > > 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. > > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] PROTEIN FOLDING
Also you must know, a lot analysis are available over the entire manual of Gromacs where all cannot be performed. Gromacs always provide you all necessary analysis but to choose which one is always your choice that suits your simulation purpose. On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta wrote: > Hi, > > > Thank you for your prompt reply. > > By clustering analysis, are you talking about gmx cluster command? > > "over particular PC sub space" > > Could you please elaborate a bit? > > Thanks a lot once again. > > Thanks, > Neha > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH > wrote: > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > > wrote: > > > > > Hi gromacs users, > > > > > > After MD simulation of protein-ligand complex for 5ns, can we view > > protein > > > folding? > > > > > > How to do it? > > > > > > I want to ascertain if there is any conformation change in protein > where > > > the ligand binds. Is it possible? > > > > > > We observe hydrogen bonds through molecular docking. Hence, I want to > > make > > > observation through MD simulation which is not obtained through > docking. > > > > > > You can perform Clustering analysis over particular PC sub space to > measure > > the structural changes. > > > > > > > > > > > Can someone help me regarding this? > > > > > > Thank you very much in advance. > > > > > > Thanks, > > > Neha > > > -- > > > 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. > > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] PROTEIN FOLDING
Ok..Thank you.. I'll extend my simulation upto 50 ns. Thanks, Neha On Tue, Dec 19, 2017 at 12:44 PM, Nikhil Maroli wrote: > After MD simulation of protein-ligand complex for 5ns, can we view protein > folding? > > mostly, NO > > Search what time range 'protein folding' is happening. > > How to do it? > > I want to ascertain if there is any conformation change in protein where > the ligand binds. Is it possible? > > > You might want to do PCA, RMSD and DSSP > > We observe hydrogen bonds through molecular docking. Hence, I want to make > observation through MD simulation which is not obtained through docking. > > > gmx hbond > > Can someone help me regarding this? > > > i really wondering what is possible in 5 ns simulation time, you may > try to extend it up to 100 ns or atleast a 50 ns. > > Thank you very much in advance. > -- > 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] PROTEIN FOLDING
You can try rmsd and gyrate plot to see the changes in your complex. It On Dec 19, 2017 2:22 PM, "RAHUL SURESH" wrote: > Also you must know, a lot analysis are available over the entire manual of > Gromacs where all cannot be performed. Gromacs always provide you all > necessary analysis but to choose which one is always your choice that suits > your simulation purpose. > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta > wrote: > > > Hi, > > > > > > Thank you for your prompt reply. > > > > By clustering analysis, are you talking about gmx cluster command? > > > > "over particular PC sub space" > > > > Could you please elaborate a bit? > > > > Thanks a lot once again. > > > > Thanks, > > Neha > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH > > wrote: > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > > > wrote: > > > > > > > Hi gromacs users, > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we view > > > protein > > > > folding? > > > > > > > > How to do it? > > > > > > > > I want to ascertain if there is any conformation change in protein > > where > > > > the ligand binds. Is it possible? > > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I want to > > > make > > > > observation through MD simulation which is not obtained through > > docking. > > > > > > > > > You can perform Clustering analysis over particular PC sub space to > > measure > > > the structural changes. > > > > > > > > > > > > > > > Can someone help me regarding this? > > > > > > > > Thank you very much in advance. > > > > > > > > Thanks, > > > > Neha > > > > -- > > > > 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. > > > > > > > -- > > > *Regards,* > > > *Rahul Suresh* > > > *Research Scholar* > > > *Bharathiar University* > > > *Coimbatore* > > > -- > > > 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. > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > 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] PROTEIN FOLDING
"You can use various supporting tools from R language to debug your trajectory but most third party software support NAMD and charmm format. You can use VMD to convert the trajectory to dcd and use R language based packages to read your trajectory" What? How is this useful or helpful? At most it confuses the OP even more. Also, the clustering analysis is unlikely to be what you want or need at this stage. Why overcomplicate? One of the simplest ways to check that there are conformational changes on a given set of atoms is by doing a RMSD analysis using the folded structure as the reference. The RMSD is somewhat degenerate, but should suffice for this purpose. You can use an index file to restrict the RMSD analysis to a particular subset of your system (the docking site, for example). You could look at the radius of gyration as well, Rg, as Aman Deep also suggests. This can either be calculated on a subset of atoms or on the entire protein. The latter could potentially be used to compare with the experimental reference obtained by SAXS, for example. Or you could calculate the SAXS curve and get a better understanding of size and shape differences between your protein and the reference, but that's more advanced stuff. J On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH wrote: > Also you must know, a lot analysis are available over the entire manual of > Gromacs where all cannot be performed. Gromacs always provide you all > necessary analysis but to choose which one is always your choice that suits > your simulation purpose. > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta > wrote: > > > Hi, > > > > > > Thank you for your prompt reply. > > > > By clustering analysis, are you talking about gmx cluster command? > > > > "over particular PC sub space" > > > > Could you please elaborate a bit? > > > > Thanks a lot once again. > > > > Thanks, > > Neha > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH > > wrote: > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > > > wrote: > > > > > > > Hi gromacs users, > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we view > > > protein > > > > folding? > > > > > > > > How to do it? > > > > > > > > I want to ascertain if there is any conformation change in protein > > where > > > > the ligand binds. Is it possible? > > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I want to > > > make > > > > observation through MD simulation which is not obtained through > > docking. > > > > > > > > > You can perform Clustering analysis over particular PC sub space to > > measure > > > the structural changes. > > > > > > > > > > > > > > > Can someone help me regarding this? > > > > > > > > Thank you very much in advance. > > > > > > > > Thanks, > > > > Neha > > > > -- > > > > 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. > > > > > > > -- > > > *Regards,* > > > *Rahul Suresh* > > > *Research Scholar* > > > *Bharathiar University* > > > *Coimbatore* > > > -- > > > 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. > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > 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-
Re: [gmx-users] PROTEIN FOLDING
Thank you Joao and Aman. I have noted the points you have suggested. Do you think analyzing DSSP would help? Thanks, Neha On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > "You can use various supporting tools from R language to debug your > trajectory but most third party software support NAMD and charmm format. > You can use VMD to convert the trajectory to dcd and use R language based > packages to read your trajectory" > > What? How is this useful or helpful? At most it confuses the OP even more. > > Also, the clustering analysis is unlikely to be what you want or need at > this stage. Why overcomplicate? One of the simplest ways to check that > there are conformational changes on a given set of atoms is by doing a RMSD > analysis using the folded structure as the reference. The RMSD is somewhat > degenerate, but should suffice for this purpose. You can use an index file > to restrict the RMSD analysis to a particular subset of your system (the > docking site, for example). > > You could look at the radius of gyration as well, Rg, as Aman Deep also > suggests. This can either be calculated on a subset of atoms or on the > entire protein. The latter could potentially be used to compare with the > experimental reference obtained by SAXS, for example. Or you could > calculate the SAXS curve and get a better understanding of size and shape > differences between your protein and the reference, but that's more > advanced stuff. > > J > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH > wrote: > > > Also you must know, a lot analysis are available over the entire manual > of > > Gromacs where all cannot be performed. Gromacs always provide you all > > necessary analysis but to choose which one is always your choice that > suits > > your simulation purpose. > > > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta > > wrote: > > > > > Hi, > > > > > > > > > Thank you for your prompt reply. > > > > > > By clustering analysis, are you talking about gmx cluster command? > > > > > > "over particular PC sub space" > > > > > > Could you please elaborate a bit? > > > > > > Thanks a lot once again. > > > > > > Thanks, > > > Neha > > > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH > > > > wrote: > > > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > > > > > wrote: > > > > > > > > > Hi gromacs users, > > > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we view > > > > protein > > > > > folding? > > > > > > > > > > How to do it? > > > > > > > > > > I want to ascertain if there is any conformation change in protein > > > where > > > > > the ligand binds. Is it possible? > > > > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I want > to > > > > make > > > > > observation through MD simulation which is not obtained through > > > docking. > > > > > > > > > > > > You can perform Clustering analysis over particular PC sub space to > > > measure > > > > the structural changes. > > > > > > > > > > > > > > > > > > > Can someone help me regarding this? > > > > > > > > > > Thank you very much in advance. > > > > > > > > > > Thanks, > > > > > Neha > > > > > -- > > > > > 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. > > > > > > > > > -- > > > > *Regards,* > > > > *Rahul Suresh* > > > > *Research Scholar* > > > > *Bharathiar University* > > > > *Coimbatore* > > > > -- > > > > 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. > > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > 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/
Re: [gmx-users] PROTEIN FOLDING
Depends. If you're interested in local folding and there are SS motifs in the region you're interested, then yes. If not, no. In terms of overall folding of the entire protein, yes it surely can be an important analysis. J On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta wrote: > Thank you Joao and Aman. > > I have noted the points you have suggested. > > Do you think analyzing DSSP would help? > > Thanks, > Neha > > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < > joao.m.a.henriq...@gmail.com> wrote: > > > "You can use various supporting tools from R language to debug your > > trajectory but most third party software support NAMD and charmm format. > > You can use VMD to convert the trajectory to dcd and use R language based > > packages to read your trajectory" > > > > What? How is this useful or helpful? At most it confuses the OP even > more. > > > > Also, the clustering analysis is unlikely to be what you want or need at > > this stage. Why overcomplicate? One of the simplest ways to check that > > there are conformational changes on a given set of atoms is by doing a > RMSD > > analysis using the folded structure as the reference. The RMSD is > somewhat > > degenerate, but should suffice for this purpose. You can use an index > file > > to restrict the RMSD analysis to a particular subset of your system (the > > docking site, for example). > > > > You could look at the radius of gyration as well, Rg, as Aman Deep also > > suggests. This can either be calculated on a subset of atoms or on the > > entire protein. The latter could potentially be used to compare with the > > experimental reference obtained by SAXS, for example. Or you could > > calculate the SAXS curve and get a better understanding of size and shape > > differences between your protein and the reference, but that's more > > advanced stuff. > > > > J > > > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH > > wrote: > > > > > Also you must know, a lot analysis are available over the entire manual > > of > > > Gromacs where all cannot be performed. Gromacs always provide you all > > > necessary analysis but to choose which one is always your choice that > > suits > > > your simulation purpose. > > > > > > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta > > > wrote: > > > > > > > Hi, > > > > > > > > > > > > Thank you for your prompt reply. > > > > > > > > By clustering analysis, are you talking about gmx cluster command? > > > > > > > > "over particular PC sub space" > > > > > > > > Could you please elaborate a bit? > > > > > > > > Thanks a lot once again. > > > > > > > > Thanks, > > > > Neha > > > > > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH < > drrahulsur...@gmail.com > > > > > > > wrote: > > > > > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta < > nehaphysic...@gmail.com > > > > > > > > wrote: > > > > > > > > > > > Hi gromacs users, > > > > > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we > view > > > > > protein > > > > > > folding? > > > > > > > > > > > > How to do it? > > > > > > > > > > > > I want to ascertain if there is any conformation change in > protein > > > > where > > > > > > the ligand binds. Is it possible? > > > > > > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I > want > > to > > > > > make > > > > > > observation through MD simulation which is not obtained through > > > > docking. > > > > > > > > > > > > > > > You can perform Clustering analysis over particular PC sub space to > > > > measure > > > > > the structural changes. > > > > > > > > > > > > > > > > > > > > > > > Can someone help me regarding this? > > > > > > > > > > > > Thank you very much in advance. > > > > > > > > > > > > Thanks, > > > > > > Neha > > > > > > -- > > > > > > 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. > > > > > > > > > > > -- > > > > > *Regards,* > > > > > *Rahul Suresh* > > > > > *Research Scholar* > > > > > *Bharathiar University* > > > > > *Coimbatore* > > > > > -- > > > > > 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
Re: [gmx-users] PROTEIN FOLDING
Hi, I tried running the simulations for 50 ns. The protein breaks (but ligand remains in the active site of the protein and it is stable throughout ) How to fix it? Thanks, Neha On Wed, Dec 20, 2017 at 6:28 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > Depends. If you're interested in local folding and there are SS motifs in > the region you're interested, then yes. If not, no. In terms of overall > folding of the entire protein, yes it surely can be an important analysis. > > J > > On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta > wrote: > > > Thank you Joao and Aman. > > > > I have noted the points you have suggested. > > > > Do you think analyzing DSSP would help? > > > > Thanks, > > Neha > > > > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < > > joao.m.a.henriq...@gmail.com> wrote: > > > > > "You can use various supporting tools from R language to debug your > > > trajectory but most third party software support NAMD and charmm > format. > > > You can use VMD to convert the trajectory to dcd and use R language > based > > > packages to read your trajectory" > > > > > > What? How is this useful or helpful? At most it confuses the OP even > > more. > > > > > > Also, the clustering analysis is unlikely to be what you want or need > at > > > this stage. Why overcomplicate? One of the simplest ways to check that > > > there are conformational changes on a given set of atoms is by doing a > > RMSD > > > analysis using the folded structure as the reference. The RMSD is > > somewhat > > > degenerate, but should suffice for this purpose. You can use an index > > file > > > to restrict the RMSD analysis to a particular subset of your system > (the > > > docking site, for example). > > > > > > You could look at the radius of gyration as well, Rg, as Aman Deep also > > > suggests. This can either be calculated on a subset of atoms or on the > > > entire protein. The latter could potentially be used to compare with > the > > > experimental reference obtained by SAXS, for example. Or you could > > > calculate the SAXS curve and get a better understanding of size and > shape > > > differences between your protein and the reference, but that's more > > > advanced stuff. > > > > > > J > > > > > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH > > > > wrote: > > > > > > > Also you must know, a lot analysis are available over the entire > manual > > > of > > > > Gromacs where all cannot be performed. Gromacs always provide you all > > > > necessary analysis but to choose which one is always your choice that > > > suits > > > > your simulation purpose. > > > > > > > > > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta > > > > wrote: > > > > > > > > > Hi, > > > > > > > > > > > > > > > Thank you for your prompt reply. > > > > > > > > > > By clustering analysis, are you talking about gmx cluster command? > > > > > > > > > > "over particular PC sub space" > > > > > > > > > > Could you please elaborate a bit? > > > > > > > > > > Thanks a lot once again. > > > > > > > > > > Thanks, > > > > > Neha > > > > > > > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH < > > drrahulsur...@gmail.com > > > > > > > > > wrote: > > > > > > > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta < > > nehaphysic...@gmail.com > > > > > > > > > > wrote: > > > > > > > > > > > > > Hi gromacs users, > > > > > > > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we > > view > > > > > > protein > > > > > > > folding? > > > > > > > > > > > > > > How to do it? > > > > > > > > > > > > > > I want to ascertain if there is any conformation change in > > protein > > > > > where > > > > > > > the ligand binds. Is it possible? > > > > > > > > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I > > want > > > to > > > > > > make > > > > > > > observation through MD simulation which is not obtained through > > > > > docking. > > > > > > > > > > > > > > > > > > You can perform Clustering analysis over particular PC sub space > to > > > > > measure > > > > > > the structural changes. > > > > > > > > > > > > > > > > > > > > > > > > > > > Can someone help me regarding this? > > > > > > > > > > > > > > Thank you very much in advance. > > > > > > > > > > > > > > Thanks, > > > > > > > Neha > > > > > > > -- > > > > > > > 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. > > > > > > > > > > > > > -- > > > > > > *Regards,* > > > > > > *Rahul Suresh* > > > > > > *Research Scholar* > > > > > > *Bharathiar University* > > > > > > *Coimbatore* > > > > > > --
Re: [gmx-users] PROTEIN FOLDING
Hi, migh be visualization error Apply pbc On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta wrote: > Hi, > > I tried running the simulations for 50 ns. > > The protein breaks (but ligand remains in the active site of the protein > and it is stable throughout ) > > How to fix it? > > Thanks, > Neha > > On Wed, Dec 20, 2017 at 6:28 PM, João Henriques < > joao.m.a.henriq...@gmail.com> wrote: > > > Depends. If you're interested in local folding and there are SS motifs in > > the region you're interested, then yes. If not, no. In terms of overall > > folding of the entire protein, yes it surely can be an important > analysis. > > > > J > > > > On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta > > wrote: > > > > > Thank you Joao and Aman. > > > > > > I have noted the points you have suggested. > > > > > > Do you think analyzing DSSP would help? > > > > > > Thanks, > > > Neha > > > > > > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < > > > joao.m.a.henriq...@gmail.com> wrote: > > > > > > > "You can use various supporting tools from R language to debug your > > > > trajectory but most third party software support NAMD and charmm > > format. > > > > You can use VMD to convert the trajectory to dcd and use R language > > based > > > > packages to read your trajectory" > > > > > > > > What? How is this useful or helpful? At most it confuses the OP even > > > more. > > > > > > > > Also, the clustering analysis is unlikely to be what you want or need > > at > > > > this stage. Why overcomplicate? One of the simplest ways to check > that > > > > there are conformational changes on a given set of atoms is by doing > a > > > RMSD > > > > analysis using the folded structure as the reference. The RMSD is > > > somewhat > > > > degenerate, but should suffice for this purpose. You can use an index > > > file > > > > to restrict the RMSD analysis to a particular subset of your system > > (the > > > > docking site, for example). > > > > > > > > You could look at the radius of gyration as well, Rg, as Aman Deep > also > > > > suggests. This can either be calculated on a subset of atoms or on > the > > > > entire protein. The latter could potentially be used to compare with > > the > > > > experimental reference obtained by SAXS, for example. Or you could > > > > calculate the SAXS curve and get a better understanding of size and > > shape > > > > differences between your protein and the reference, but that's more > > > > advanced stuff. > > > > > > > > J > > > > > > > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH < > drrahulsur...@gmail.com > > > > > > > wrote: > > > > > > > > > Also you must know, a lot analysis are available over the entire > > manual > > > > of > > > > > Gromacs where all cannot be performed. Gromacs always provide you > all > > > > > necessary analysis but to choose which one is always your choice > that > > > > suits > > > > > your simulation purpose. > > > > > > > > > > > > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta < > nehaphysic...@gmail.com> > > > > > wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > > > > > > > Thank you for your prompt reply. > > > > > > > > > > > > By clustering analysis, are you talking about gmx cluster > command? > > > > > > > > > > > > "over particular PC sub space" > > > > > > > > > > > > Could you please elaborate a bit? > > > > > > > > > > > > Thanks a lot once again. > > > > > > > > > > > > Thanks, > > > > > > Neha > > > > > > > > > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH < > > > drrahulsur...@gmail.com > > > > > > > > > > > wrote: > > > > > > > > > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta < > > > nehaphysic...@gmail.com > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > Hi gromacs users, > > > > > > > > > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we > > > view > > > > > > > protein > > > > > > > > folding? > > > > > > > > > > > > > > > > How to do it? > > > > > > > > > > > > > > > > I want to ascertain if there is any conformation change in > > > protein > > > > > > where > > > > > > > > the ligand binds. Is it possible? > > > > > > > > > > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I > > > want > > > > to > > > > > > > make > > > > > > > > observation through MD simulation which is not obtained > through > > > > > > docking. > > > > > > > > > > > > > > > > > > > > > You can perform Clustering analysis over particular PC sub > space > > to > > > > > > measure > > > > > > > the structural changes. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Can someone help me regarding this? > > > > > > > > > > > > > > > > Thank you very much in advance. > > > > > > > > > > > > > > > > Thanks, > > > > > > > > Neha > > > > > > > > -- > > > > > > > > Gromacs Users mailing list > > > > > > > > > > > > > > > > * Please search the archive at > > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > > before > > > > > > > > posting! > > > > > > > > > > >
Re: [gmx-users] PROTEIN FOLDING
I gave gmx trjconv -pbc nojump -s prd.gro -f prd.xtc -e 5.0 -n index.ndx -o PRD.pdb Is there any other alternate command? Thanks, Neha On Thu, Dec 28, 2017 at 11:30 AM, RAHUL SURESH wrote: > Hi, > > migh be visualization error > > Apply pbc > > On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta > wrote: > > > Hi, > > > > I tried running the simulations for 50 ns. > > > > The protein breaks (but ligand remains in the active site of the protein > > and it is stable throughout ) > > > > How to fix it? > > > > Thanks, > > Neha > > > > On Wed, Dec 20, 2017 at 6:28 PM, João Henriques < > > joao.m.a.henriq...@gmail.com> wrote: > > > > > Depends. If you're interested in local folding and there are SS motifs > in > > > the region you're interested, then yes. If not, no. In terms of overall > > > folding of the entire protein, yes it surely can be an important > > analysis. > > > > > > J > > > > > > On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta > > > wrote: > > > > > > > Thank you Joao and Aman. > > > > > > > > I have noted the points you have suggested. > > > > > > > > Do you think analyzing DSSP would help? > > > > > > > > Thanks, > > > > Neha > > > > > > > > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < > > > > joao.m.a.henriq...@gmail.com> wrote: > > > > > > > > > "You can use various supporting tools from R language to debug your > > > > > trajectory but most third party software support NAMD and charmm > > > format. > > > > > You can use VMD to convert the trajectory to dcd and use R language > > > based > > > > > packages to read your trajectory" > > > > > > > > > > What? How is this useful or helpful? At most it confuses the OP > even > > > > more. > > > > > > > > > > Also, the clustering analysis is unlikely to be what you want or > need > > > at > > > > > this stage. Why overcomplicate? One of the simplest ways to check > > that > > > > > there are conformational changes on a given set of atoms is by > doing > > a > > > > RMSD > > > > > analysis using the folded structure as the reference. The RMSD is > > > > somewhat > > > > > degenerate, but should suffice for this purpose. You can use an > index > > > > file > > > > > to restrict the RMSD analysis to a particular subset of your system > > > (the > > > > > docking site, for example). > > > > > > > > > > You could look at the radius of gyration as well, Rg, as Aman Deep > > also > > > > > suggests. This can either be calculated on a subset of atoms or on > > the > > > > > entire protein. The latter could potentially be used to compare > with > > > the > > > > > experimental reference obtained by SAXS, for example. Or you could > > > > > calculate the SAXS curve and get a better understanding of size and > > > shape > > > > > differences between your protein and the reference, but that's more > > > > > advanced stuff. > > > > > > > > > > J > > > > > > > > > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH < > > drrahulsur...@gmail.com > > > > > > > > > wrote: > > > > > > > > > > > Also you must know, a lot analysis are available over the entire > > > manual > > > > > of > > > > > > Gromacs where all cannot be performed. Gromacs always provide you > > all > > > > > > necessary analysis but to choose which one is always your choice > > that > > > > > suits > > > > > > your simulation purpose. > > > > > > > > > > > > > > > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta < > > nehaphysic...@gmail.com> > > > > > > wrote: > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > > > > > > > > Thank you for your prompt reply. > > > > > > > > > > > > > > By clustering analysis, are you talking about gmx cluster > > command? > > > > > > > > > > > > > > "over particular PC sub space" > > > > > > > > > > > > > > Could you please elaborate a bit? > > > > > > > > > > > > > > Thanks a lot once again. > > > > > > > > > > > > > > Thanks, > > > > > > > Neha > > > > > > > > > > > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH < > > > > drrahulsur...@gmail.com > > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta < > > > > nehaphysic...@gmail.com > > > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > > > Hi gromacs users, > > > > > > > > > > > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can > we > > > > view > > > > > > > > protein > > > > > > > > > folding? > > > > > > > > > > > > > > > > > > How to do it? > > > > > > > > > > > > > > > > > > I want to ascertain if there is any conformation change in > > > > protein > > > > > > > where > > > > > > > > > the ligand binds. Is it possible? > > > > > > > > > > > > > > > > > > We observe hydrogen bonds through molecular docking. > Hence, I > > > > want > > > > > to > > > > > > > > make > > > > > > > > > observation through MD simulation which is not obtained > > through > > > > > > > docking. > > > > > > > > > > > > > > > > > > > > > > > > You can perform Clustering analysis over particular PC sub > > space > > > to > > > > > > >
Re: [gmx-users] PROTEIN FOLDING
On 12/28/17 6:25 AM, Neha Gupta wrote: I gave gmx trjconv -pbc nojump -s prd.gro -f prd.xtc -e 5.0 -n index.ndx -o PRD.pdb Is there any other alternate command? http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin Thanks, Neha On Thu, Dec 28, 2017 at 11:30 AM, RAHUL SURESH wrote: Hi, migh be visualization error Apply pbc On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta wrote: Hi, I tried running the simulations for 50 ns. The protein breaks (but ligand remains in the active site of the protein and it is stable throughout ) How to fix it? Thanks, Neha On Wed, Dec 20, 2017 at 6:28 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: Depends. If you're interested in local folding and there are SS motifs in the region you're interested, then yes. If not, no. In terms of overall folding of the entire protein, yes it surely can be an important analysis. J On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta wrote: Thank you Joao and Aman. I have noted the points you have suggested. Do you think analyzing DSSP would help? Thanks, Neha On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: "You can use various supporting tools from R language to debug your trajectory but most third party software support NAMD and charmm format. You can use VMD to convert the trajectory to dcd and use R language based packages to read your trajectory" What? How is this useful or helpful? At most it confuses the OP even more. Also, the clustering analysis is unlikely to be what you want or need at this stage. Why overcomplicate? One of the simplest ways to check that there are conformational changes on a given set of atoms is by doing a RMSD analysis using the folded structure as the reference. The RMSD is somewhat degenerate, but should suffice for this purpose. You can use an index file to restrict the RMSD analysis to a particular subset of your system (the docking site, for example). You could look at the radius of gyration as well, Rg, as Aman Deep also suggests. This can either be calculated on a subset of atoms or on the entire protein. The latter could potentially be used to compare with the experimental reference obtained by SAXS, for example. Or you could calculate the SAXS curve and get a better understanding of size and shape differences between your protein and the reference, but that's more advanced stuff. J On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH < drrahulsur...@gmail.com wrote: Also you must know, a lot analysis are available over the entire manual of Gromacs where all cannot be performed. Gromacs always provide you all necessary analysis but to choose which one is always your choice that suits your simulation purpose. On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta < nehaphysic...@gmail.com> wrote: Hi, Thank you for your prompt reply. By clustering analysis, are you talking about gmx cluster command? "over particular PC sub space" Could you please elaborate a bit? Thanks a lot once again. Thanks, Neha On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH < drrahulsur...@gmail.com wrote: On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta < nehaphysic...@gmail.com wrote: Hi gromacs users, After MD simulation of protein-ligand complex for 5ns, can we view protein folding? How to do it? I want to ascertain if there is any conformation change in protein where the ligand binds. Is it possible? We observe hydrogen bonds through molecular docking. Hence, I want to make observation through MD simulation which is not obtained through docking. You can perform Clustering analysis over particular PC sub space to measure the structural changes. Can someone help me regarding this? Thank you very much in advance. Thanks, Neha -- 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. -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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.or
Re: [gmx-users] PROTEIN FOLDING
Do it multiple times by center the ligand first and then protein in the other step,while using pbc. Use -pbc mol option in one of the step to get the whole molecule. Thanks On Thu, Dec 28, 2017 at 6:26 AM Neha Gupta wrote: > I gave > > gmx trjconv -pbc nojump -s prd.gro -f prd.xtc -e 5.0 -n index.ndx -o > PRD.pdb > > Is there any other alternate command? > > Thanks, > Neha > > On Thu, Dec 28, 2017 at 11:30 AM, RAHUL SURESH > wrote: > > > Hi, > > > > migh be visualization error > > > > Apply pbc > > > > On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta > > wrote: > > > > > Hi, > > > > > > I tried running the simulations for 50 ns. > > > > > > The protein breaks (but ligand remains in the active site of the > protein > > > and it is stable throughout ) > > > > > > How to fix it? > > > > > > Thanks, > > > Neha > > > > > > On Wed, Dec 20, 2017 at 6:28 PM, João Henriques < > > > joao.m.a.henriq...@gmail.com> wrote: > > > > > > > Depends. If you're interested in local folding and there are SS > motifs > > in > > > > the region you're interested, then yes. If not, no. In terms of > overall > > > > folding of the entire protein, yes it surely can be an important > > > analysis. > > > > > > > > J > > > > > > > > On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta > > > > > wrote: > > > > > > > > > Thank you Joao and Aman. > > > > > > > > > > I have noted the points you have suggested. > > > > > > > > > > Do you think analyzing DSSP would help? > > > > > > > > > > Thanks, > > > > > Neha > > > > > > > > > > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < > > > > > joao.m.a.henriq...@gmail.com> wrote: > > > > > > > > > > > "You can use various supporting tools from R language to debug > your > > > > > > trajectory but most third party software support NAMD and charmm > > > > format. > > > > > > You can use VMD to convert the trajectory to dcd and use R > language > > > > based > > > > > > packages to read your trajectory" > > > > > > > > > > > > What? How is this useful or helpful? At most it confuses the OP > > even > > > > > more. > > > > > > > > > > > > Also, the clustering analysis is unlikely to be what you want or > > need > > > > at > > > > > > this stage. Why overcomplicate? One of the simplest ways to check > > > that > > > > > > there are conformational changes on a given set of atoms is by > > doing > > > a > > > > > RMSD > > > > > > analysis using the folded structure as the reference. The RMSD is > > > > > somewhat > > > > > > degenerate, but should suffice for this purpose. You can use an > > index > > > > > file > > > > > > to restrict the RMSD analysis to a particular subset of your > system > > > > (the > > > > > > docking site, for example). > > > > > > > > > > > > You could look at the radius of gyration as well, Rg, as Aman > Deep > > > also > > > > > > suggests. This can either be calculated on a subset of atoms or > on > > > the > > > > > > entire protein. The latter could potentially be used to compare > > with > > > > the > > > > > > experimental reference obtained by SAXS, for example. Or you > could > > > > > > calculate the SAXS curve and get a better understanding of size > and > > > > shape > > > > > > differences between your protein and the reference, but that's > more > > > > > > advanced stuff. > > > > > > > > > > > > J > > > > > > > > > > > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH < > > > drrahulsur...@gmail.com > > > > > > > > > > > wrote: > > > > > > > > > > > > > Also you must know, a lot analysis are available over the > entire > > > > manual > > > > > > of > > > > > > > Gromacs where all cannot be performed. Gromacs always provide > you > > > all > > > > > > > necessary analysis but to choose which one is always your > choice > > > that > > > > > > suits > > > > > > > your simulation purpose. > > > > > > > > > > > > > > > > > > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta < > > > nehaphysic...@gmail.com> > > > > > > > wrote: > > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > > > > > > > > > > > Thank you for your prompt reply. > > > > > > > > > > > > > > > > By clustering analysis, are you talking about gmx cluster > > > command? > > > > > > > > > > > > > > > > "over particular PC sub space" > > > > > > > > > > > > > > > > Could you please elaborate a bit? > > > > > > > > > > > > > > > > Thanks a lot once again. > > > > > > > > > > > > > > > > Thanks, > > > > > > > > Neha > > > > > > > > > > > > > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH < > > > > > drrahulsur...@gmail.com > > > > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta < > > > > > nehaphysic...@gmail.com > > > > > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > > > > > Hi gromacs users, > > > > > > > > > > > > > > > > > > > > After MD simulation of protein-ligand complex for 5ns, > can > > we > > > > > view > > > > > > > > > protein > > > > > > > > > > folding? > > > > > > > > > > > > > > > > > > > > How to do it? > >
Re: [gmx-users] PROTEIN FOLDING
Hi, I tried this one gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n index.ndx This asks me to select a group fro clustering and then select a group for output.. What should I select first and then next? Thanks, Neha On Thu, Dec 28, 2017 at 5:44 PM, Lakshman Ji Verma wrote: > Do it multiple times by center the ligand first and then protein in the > other step,while using pbc. Use -pbc mol option in one of the step to get > the whole molecule. > > Thanks > > On Thu, Dec 28, 2017 at 6:26 AM Neha Gupta > wrote: > > > I gave > > > > gmx trjconv -pbc nojump -s prd.gro -f prd.xtc -e 5.0 -n index.ndx -o > > PRD.pdb > > > > Is there any other alternate command? > > > > Thanks, > > Neha > > > > On Thu, Dec 28, 2017 at 11:30 AM, RAHUL SURESH > > wrote: > > > > > Hi, > > > > > > migh be visualization error > > > > > > Apply pbc > > > > > > On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta > > > wrote: > > > > > > > Hi, > > > > > > > > I tried running the simulations for 50 ns. > > > > > > > > The protein breaks (but ligand remains in the active site of the > > protein > > > > and it is stable throughout ) > > > > > > > > How to fix it? > > > > > > > > Thanks, > > > > Neha > > > > > > > > On Wed, Dec 20, 2017 at 6:28 PM, João Henriques < > > > > joao.m.a.henriq...@gmail.com> wrote: > > > > > > > > > Depends. If you're interested in local folding and there are SS > > motifs > > > in > > > > > the region you're interested, then yes. If not, no. In terms of > > overall > > > > > folding of the entire protein, yes it surely can be an important > > > > analysis. > > > > > > > > > > J > > > > > > > > > > On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta < > nehaphysic...@gmail.com > > > > > > > > wrote: > > > > > > > > > > > Thank you Joao and Aman. > > > > > > > > > > > > I have noted the points you have suggested. > > > > > > > > > > > > Do you think analyzing DSSP would help? > > > > > > > > > > > > Thanks, > > > > > > Neha > > > > > > > > > > > > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < > > > > > > joao.m.a.henriq...@gmail.com> wrote: > > > > > > > > > > > > > "You can use various supporting tools from R language to debug > > your > > > > > > > trajectory but most third party software support NAMD and > charmm > > > > > format. > > > > > > > You can use VMD to convert the trajectory to dcd and use R > > language > > > > > based > > > > > > > packages to read your trajectory" > > > > > > > > > > > > > > What? How is this useful or helpful? At most it confuses the OP > > > even > > > > > > more. > > > > > > > > > > > > > > Also, the clustering analysis is unlikely to be what you want > or > > > need > > > > > at > > > > > > > this stage. Why overcomplicate? One of the simplest ways to > check > > > > that > > > > > > > there are conformational changes on a given set of atoms is by > > > doing > > > > a > > > > > > RMSD > > > > > > > analysis using the folded structure as the reference. The RMSD > is > > > > > > somewhat > > > > > > > degenerate, but should suffice for this purpose. You can use an > > > index > > > > > > file > > > > > > > to restrict the RMSD analysis to a particular subset of your > > system > > > > > (the > > > > > > > docking site, for example). > > > > > > > > > > > > > > You could look at the radius of gyration as well, Rg, as Aman > > Deep > > > > also > > > > > > > suggests. This can either be calculated on a subset of atoms or > > on > > > > the > > > > > > > entire protein. The latter could potentially be used to compare > > > with > > > > > the > > > > > > > experimental reference obtained by SAXS, for example. Or you > > could > > > > > > > calculate the SAXS curve and get a better understanding of size > > and > > > > > shape > > > > > > > differences between your protein and the reference, but that's > > more > > > > > > > advanced stuff. > > > > > > > > > > > > > > J > > > > > > > > > > > > > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH < > > > > drrahulsur...@gmail.com > > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > Also you must know, a lot analysis are available over the > > entire > > > > > manual > > > > > > > of > > > > > > > > Gromacs where all cannot be performed. Gromacs always provide > > you > > > > all > > > > > > > > necessary analysis but to choose which one is always your > > choice > > > > that > > > > > > > suits > > > > > > > > your simulation purpose. > > > > > > > > > > > > > > > > > > > > > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta < > > > > nehaphysic...@gmail.com> > > > > > > > > wrote: > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > > > > > > > > > > > > > > Thank you for your prompt reply. > > > > > > > > > > > > > > > > > > By clustering analysis, are you talking about gmx cluster > > > > command? > > > > > > > > > > > > > > > > > > "over particular PC sub space" > > > > > > > > > > > > > > > > > > Could you please elaborate a bit? > > > > > > > > > > > > > > > > > > Thanks a lot once
Re: [gmx-users] PROTEIN FOLDING
On 12/28/17 8:33 AM, Neha Gupta wrote: Hi, I tried this one gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n index.ndx This asks me to select a group fro clustering and then select a group for output.. What should I select first and then next? Clustering isn't relevant. Your situation is much simpler than it's being made out to be. 1. Make molecules whole 2. Remove jumps 3. Center -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] PROTEIN FOLDING
Hi Justin, Can you please let me know the exact commands? None of the commands which I tried are working... Thanks, Neha On Thu, Dec 28, 2017 at 7:04 PM, Justin Lemkul wrote: > > > On 12/28/17 8:33 AM, Neha Gupta wrote: > >> Hi, >> >> I tried this one >> >> gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n >> index.ndx >> >> This asks me to select a group fro clustering and then select a group for >> output.. >> >> What should I select first and then next? >> > > Clustering isn't relevant. Your situation is much simpler than it's being > made out to be. > > 1. Make molecules whole > 2. Remove jumps > 3. Center > > -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. > -- 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] PROTEIN FOLDING
gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc nojump -o trajclust.xtc -n index.ndx -center Please read this first: http://manual.gromacs.org/documentation/2016.1/onlinehelp/gmx-trjconv.html trjconv is quite powerful, so it worth to know available options. -Alexandr On 30/12/2017 16:37, Neha Gupta wrote: Hi Justin, Can you please let me know the exact commands? None of the commands which I tried are working... Thanks, Neha On Thu, Dec 28, 2017 at 7:04 PM, Justin Lemkul wrote: On 12/28/17 8:33 AM, Neha Gupta wrote: Hi, I tried this one gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n index.ndx This asks me to select a group fro clustering and then select a group for output.. What should I select first and then next? Clustering isn't relevant. Your situation is much simpler than it's being made out to be. 1. Make molecules whole 2. Remove jumps 3. Center -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. -- 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] PROTEIN FOLDING
On 12/30/17 10:47 AM, Alexandr Nasedkin wrote: gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc nojump -o trajclust.xtc -n index.ndx -center Removing jumps and centering simultaneously should be considered mutually exclusive. One usually needs a few rounds of trjconv, e.g. gmx trjconv -pbc whole gmx trjconv -pbc nojump gmx trjconv -pbc mol -center Almost always does the trick for simple systems. -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] PROTEIN FOLDING
At first, I gave, gmx trjconv -pbc whole -s prd.tpr -f prd.xtc -o trajwhole.xtc I selected "system" for output It says Program gmx trjconv, VERSION 5.1.4 Source code file: /cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/gmx_trjconv.c, line: 1322 Fatal error: Index[6376] 6377 is larger than the number of atoms in the trajectory file (6376). There is a mismatch in the contents of your -f, -s and/or -n files. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Which index number should I select for all the three commands mentioned above? Thanks, Neha On Sat, Dec 30, 2017 at 9:42 PM, Justin Lemkul wrote: > > > On 12/30/17 10:47 AM, Alexandr Nasedkin wrote: > >> gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc nojump -o trajclust.xtc -n >> index.ndx -center >> >> > Removing jumps and centering simultaneously should be considered mutually > exclusive. One usually needs a few rounds of trjconv, e.g. > > gmx trjconv -pbc whole > gmx trjconv -pbc nojump > gmx trjconv -pbc mol -center > > Almost always does the trick for simple systems. > > -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. > -- 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] PROTEIN FOLDING
On 12/30/17 11:44 PM, Neha Gupta wrote: At first, I gave, gmx trjconv -pbc whole -s prd.tpr -f prd.xtc -o trajwhole.xtc I selected "system" for output It says Program gmx trjconv, VERSION 5.1.4 Source code file: /cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/gmx_trjconv.c, line: 1322 Fatal error: Index[6376] 6377 is larger than the number of atoms in the trajectory file (6376). There is a mismatch in the contents of your -f, -s and/or -n files. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Which index number should I select for all the three commands mentioned above? No command is going to work if the contents of the .tpr and .xtc do not match. Either you've mixed up your files or you didn't save all coordinates during the run, in which case you need to make a matching .tpr file. gmx check may provide some clues, but at present it's hard to know what has gone wrong. -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] PROTEIN FOLDING
Yes, you can open all structural output files with VMD. Or Chimera (tools MD so on). On Thursday, April 6, 2017 9:56 AM, Neha Gupta wrote: Hi gromacs users, I have run 2ns simulation of protein ligand complex using NVT ensemble (after equilibration). I want to know whether there is a structural/conformational change in the protein especially in the active site where, the ligand forms hydrogen bonds with the protein during simulation. Can we visualize it? Is it possible? Please let me know. Thanks, Neha -- 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] PROTEIN FOLDING IN GROMACS
Hi gromacs users, What are the steps for simulation to observe protein folding in gromacs? Thanks, Subashini.K -- 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.