[gmx-users] protein and ligand is not forming complex after completing simulation
Marlon Sidore
marlon.sidore at gmail.com
Wed Jul 27 17:42:13 CEST 2016
system for all outputs
for centering (the first of the second command) you should probably select
protein
Marlon Sidore
PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France
2016-07-27 17:25 GMT+02:00 Swagata Patra <swagataliza at gmail.com>:
> so when the program ask to select a group, what should i select? system or
> protein for the first command?
>
> What should I select for the second command? they are asking for selecting
> 2 groups.
>
> On Wed, Jul 27, 2016 at 8:45 PM, Marlon Sidore <marlon.sidore at gmail.com>
> wrote:
>
> > Sorry I just realized I copypasted the -o without noticing it was a pdb.
> > You'll want use the output of each command (a .xtc) as input for each
> > following command. You also probably don't need the index file with -n.
> >
> > trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj0.xtc -pbc
> nojump
> >
> > trjconv_d -s md_0_1.tpr -f trj0.xtc -n index.ndx -o trj1.xtc -center
> [[Here
> > center on your protein for example]]
> >
> > trjconv_d -s md_0_1.tpr -f trj1.xtc -n index.ndx -o trj2.xtc -pbc mol
> >
> > Marlon Sidore
> >
> >
> > PhD Student
> > Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
> > CNRS - UMR7255
> > 31, Chemin Joseph Aiguier
> > 13402 cedex 20 Marseille
> > France
> >
> >
> > 2016-07-27 16:46 GMT+02:00 Swagata Patra <swagataliza at gmail.com>:
> >
> > > Hi Marlon.
> > > The commands that you gave
> > > trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj0.pdb -pbc
> > nojump
> > >
> > > trjconv_d -s md_0_1.tpr -f trj0.xtc -n index.ndx -o trj1.pdb -center
> > [[Here
> > > center on your protein for example]]
> > >
> > > trjconv_d -s md_0_1.tpr -f trj1.xtc -n index.ndx -o trj2.pdb -pbc mol
> > >
> > > From where will get trj0.xtc file?
> > >
> > > On Wed, Jul 27, 2016 at 7:30 PM, Swagata Patra <swagataliza at gmail.com>
> > > wrote:
> > >
> > > > Thank you Marlon for your suggestion. It really helped a lot.
> > > >
> > > > On Wed, Jul 27, 2016 at 7:28 PM, Swagata Patra <
> swagataliza at gmail.com>
> > > > wrote:
> > > >
> > > >> thank you James and Felipe for your suggestion. It really helped me
> a
> > > >> lot to understand the situation.
> > > >> I am trying to resolve the problem.
> > > >>
> > > >> On Wed, Jul 27, 2016 at 6:00 PM, Felipe Merino <
> > > >> felipe.merino at mpi-dortmund.mpg.de> wrote:
> > > >>
> > > >>> Hey,
> > > >>>
> > > >>> Of course you can always use VMD, for example, to check several
> > > adjacent
> > > >>> copies of the simulation cell in order to see if your problem is
> PBC
> > > or not.
> > > >>>
> > > >>> Felipe
> > > >>>
> > > >>>
> > > >>> On 27/07/16 14:21, Justin Lemkul wrote:
> > > >>>
> > > >>>>
> > > >>>>
> > > >>>> On 7/27/16 8:18 AM, Swagata Patra wrote:
> > > >>>>
> > > >>>>> For trjconv i used the following command:
> > > >>>>>
> > > >>>>> trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj.pdb
> -pbc
> > > mol
> > > >>>>> -ur
> > > >>>>> compact -dt 30000
> > > >>>>>
> > > >>>>>
> > > >>>> The PBC fitting routines sometimes struggle with large -dt. You're
> > > >>>> basically just trying to dump out the final frame, which is
> > redundant
> > > with
> > > >>>> what you're doing below. If you want to obtain a PBC-corrected
> > > trajectory,
> > > >>>> follow the link I provided.
> > > >>>>
> > > >>>> For editconf I simply used : editconf_d -f md_0_1.gro -o
> md_0_1.pdb
> > > >>>>>
> > > >>>>> I have analyzed the H-bonds between protein and ligand, there
> > showing
> > > >>>>> formation of H-bonds.
> > > >>>>>
> > > >>>>> if ligand is dissociating, what could be the reason?
> > > >>>>>
> > > >>>>>
> > > >>>> Bad topology, incorrect run settings, etc. But from the simple
> > matter
> > > >>>> of disagreement above, I doubt there's actually a problem. Nearly
> > > always,
> > > >>>> "dissociation" is just a PBC issue that needs to be handled
> > carefully.
> > > >>>>
> > > >>>> -Justin
> > > >>>>
> > > >>>>
> > > >>>>> On Wed, Jul 27, 2016 at 5:40 PM, <jkrieger at mrc-lmb.cam.ac.uk>
> > wrote:
> > > >>>>>
> > > >>>>> Hi Swagata,
> > > >>>>>>
> > > >>>>>> Perhaps your ligand is dissociating during the simulation. What
> > > >>>>>> frames are
> > > >>>>>> you looking at with trjconv and editconf? If these are different
> > you
> > > >>>>>> may
> > > >>>>>> be seeing bound and unbound snapshots.
> > > >>>>>>
> > > >>>>>> Best wishes
> > > >>>>>> James
> > > >>>>>>
> > > >>>>>> hi everyone,
> > > >>>>>>>
> > > >>>>>>> I simulated protein-ligand complex for 30ns and then visualize
> > the
> > > >>>>>>> complex
> > > >>>>>>> after simulation in pymol.
> > > >>>>>>>
> > > >>>>>>> I got the .pdb file using two commands from final simulated
> file.
> > > >>>>>>> One is using trjconv, from .xtc to .pdb. When I am visualizing
> > this
> > > >>>>>>> .pdb
> > > >>>>>>> file, protein and ligand has not formed any complex.
> > > >>>>>>> Another one is using editconf, from .gro to .pdb. When I am
> > > >>>>>>> visualizing
> > > >>>>>>> this .pdb file, protein and ligand formed complex.
> > > >>>>>>>
> > > >>>>>>> Why is this happening? Can anyone explain it?
> > > >>>>>>>
> > > >>>>>>> Thanks in advance.
> > > >>>>>>>
> > > >>>>>>> --
> > > >>>>>>> Swagata Patra
> > > >>>>>>> M.Tech (Biotech)
> > > >>>>>>> JRF
> > > >>>>>>> IIT Guwahati
> > > >>>>>>> --
> > > >>>>>>> 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-request at 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-request at gromacs.org.
> > > >>>>>>
> > > >>>>>>
> > > >>>>>
> > > >>>>>
> > > >>>>>
> > > >>>>
> > > >>> --
> > > >>> Felipe Merino
> > > >>> Max Planck Institute for Molecular Physiology
> > > >>> Department of Structural Biochemistry
> > > >>> Otto-Hahn-Str. 11
> > > >>> 44227 Dortmund
> > > >>> Phone: +49 231 133 2315
> > > >>>
> > > >>>
> > > >>> --
> > > >>> 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-request at gromacs.org.
> > > >>>
> > > >>
> > > >>
> > > >>
> > > >> --
> > > >> Swagata Patra
> > > >> M.Tech (Biotech)
> > > >> JRF
> > > >> IIT Guwahati
> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > Swagata Patra
> > > > M.Tech (Biotech)
> > > > JRF
> > > > IIT Guwahati
> > > >
> > >
> > >
> > >
> > > --
> > > Swagata Patra
> > > M.Tech (Biotech)
> > > JRF
> > > IIT Guwahati
> > > --
> > > 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-request at 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-request at gromacs.org.
> >
>
>
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
> --
> 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-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list