I gave gmx trjconv -pbc nojump -s prd.gro -f prd.xtc -e 50000.0 -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 <drrahulsur...@gmail.com> wrote: > Hi, > > migh be visualization error > > Apply pbc > > On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta <nehaphysic...@gmail.com> > 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 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? 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