Hi, It's hard for anyone to know what you're doing and seeing unless you share actual command lines, and upload your resulting graphs to a file-sharing service and provide a link (the list does not take attachments)
Mark On Tue, 15 Nov 2016 08:51 Khadija Amine <[email protected]> wrote: > Ok I will try that. > > There is a way to specify the regions to plot in RMSF using rms tool? > > Thank you > > *Khadija AMINE* > > > *Computational Biology* > *Postdoctoral Research Associate* > *Carnegie Mellon University* > > On Tue, Nov 15, 2016 at 10:40 AM, Khadija Amine <[email protected]> > wrote: > > > Hello, > > > > Can someone show me how can I proceed? > > > > Thank you > > > > *Khadija AMINE* > > > > > > *Computational Biology* > > *Postdoctoral Research Associate* > > *Carnegie Mellon University* > > > > On Mon, Nov 14, 2016 at 2:33 PM, Khadija Amine <[email protected]> > > wrote: > > > >> Dear Gromacs users, > >> > >> I need your help regarding MD simulation of two chains protein. > >> The chain A is 2-78 aa, and the chain B is 1-168 aa. > >> > >> I started with the pdb file where there is specified names of the two > >> chains as A and B. > >> > >> I did solvation of my system in a cubic box, I tried to open the > >> pdb file issued from this step I didn't find the column specifying the > >> chain names. > >> > >> I run 20 ns of MD for this protein. The RMSF plot of the protein seems > >> to be overlapping from 1 to 78 and the rest of the residues flctuation > >> is good. > >> > >> As it is the first time am facing such issues with protein with two > >> chains, how can I avoid such overlap in RMSF plot? > >> > >> Is this linked to the chains numbering issued after writing the > topology. > >> > >> Thank you > >> > >> *Khadija AMINE* > >> > >> > >> *Computational Biology* > >> *Postdoctoral Research Associate* > >> *Carnegie Mellon University* > >> > > > > > -- > 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 [email protected]. > -- 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 [email protected].
