[gmx-users] Protein-Ligand in bilayer

[Mark Abraham]

Hi,

None of those are GROMACS tools, so you will probably do better asking
elsewhere. But why not generate the topology after the ligands atoms get
sorted?

Mark

On Sat, Aug 11, 2018, 04:18 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

> Hi Dr. Mark.
>
> The docked complex ( docked using auto dock ) when given as input in
> charmm-gui, it ask for either mol2 file or top and prm file generated using
> paramchem.
>
> But then it shows some atom number mismatch and couldn’t proceed further.
>
> The docked ligand ( pdbqt ) is converted  to pdb format ( by adding
> hydrogen ) using open babel.
>
> Thank you
>
> On Sat, 11 Aug 2018 at 5:01 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Does CHARMM-GUI not provide a output coordinate file that matches the
> > generated topology file? I don't know why you find its change of
> ordering a
> > problem.
> >
> > Mark
> >
> > On Thu, Aug 9, 2018, 18:48 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:
> >
> > > Hi users.
> > >
> > > It look so complicated to carry out a protein ligand simulation in
> Lipid
> > > bilayer system using charmm ff. I have a ligand with 27 atoms (
> includes
> > > Hydrogen ). The initial structure (monomer)  is simulated in popc
> > > constructed using charmm gui web page. To construct the same for the
> > > portein-ligand complex is too tedious and very problematic.
> > > The protein-ligand complex is constructed using auto dock from the mol2
> > > file download from Zinc database. The complex structure then is
> uploaded
> > to
> > > charmm gui and the atom number varies with the mol2 file and pdb file.
> I
> > > find no way to change the atom order or numbering.
> > >
> > > I feel I m taking a wrong way in these type of simulations. What can be
> > the
> > > better way to do such simulations?
> > >
> > > --
> > > *Regards,*
> > > *Rahul *
> > > --
> > > 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.
> >
> --
> *Regards,*
> *Rahul *
> --
> 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.