VMD has no knowledge of bonds, as all you fed it was a coordinate file. It makes guesses based on the separation of the atoms which atoms are bonded or not. So no bonds are being broken.
Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 27 May 2019 at 15:12, Dilip.H.N <cy16f01.di...@nitk.edu.in> wrote: > > Hi all, > I have a capped peptide and when i solvate the system with water and > visualize it in vmd, the bonds between the peptide and corresponding capped > N and C terminal groups is not seen (or) broken. > Whereas before solvating the system, the bonds between the peptide and > corresponding capped N and C terminals are intact when visualized in vmd. > > Why is this happening? After solvating the peptide system, why are the > bonds between peptide and capped terminal groups getting broken.? > > How can i solve this issue...? > > Any suggestions are highly appreciated. > Thank you. > > --- > With Best Regards, > > Dilip.H.N > Ph.D. Student. > > > [image: Mailtrack] > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> > Sender > notified by > Mailtrack > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> > 27/05/19, > 10:33:05 > -- > 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.
