I have modelled my protein using homology modeling software & then have used gromacs for energy minimization.
gmx trjconv -f md22.xtc -s md22.tpr -o md22.pdb then I have choosen only protein from the options On Sat, May 14, 2016 at 3:55 PM, Pratiti Bhadra <pratiti.bha...@gmail.com> wrote: > How many frames do u save using trjconv?. Can you please post your full > trjconv command here. > On 14 May 2016 18:21, "Chalaoux, Francois-Regis" < > francois-regis.chala...@evotec.com> wrote: > > > What is your protein, PDB Id ? > > > > FR. > > > > > Le 14 mai 2016 à 12:04:09, Upasana Ray <upasanaray...@gmail.com> a > > écrit : > > > > > > yes I have removed water & the pdb file only contains protein > > > > > > On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis < > > > francois-regis.chala...@evotec.com> wrote: > > > > > >> Hi, > > >> > > >> Did you removed Water ? > > >> Check also there is no other protein in the same file. > > >> > > >> FR. > > >> > > >>> Le 14 mai 2016 à 07:04:15, Upasana Ray <upasanaray...@gmail.com> a > > >> écrit : > > >>> > > >>> Dear user, > > >>> > > >>> I have generated my final protein.pdb file by using trjconv command > > from > > >>> .xtc file. The size of my pdb file is 0.98 GB, so whenever I am > opening > > >> it > > >>> for docking purpose my computer is freezing. Now how can I reduce my > > pdb > > >>> file size from GB to MB for using it properly. please help me to > deal > > >>> with this problem. > > >>> -- > > >>> 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. > > >> > > > -- > > > 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. > -- > 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.