[gmx-users] (no subject)

[Mark Abraham]

Hi,

Follow ATB's directions for how to use the files it produces. If ATB is
creating a new atom type, then it will be supplying parameters that belong
in the [atomtypes] directive, and their site needs to give you instructions
for how to get those recognized. Search their website and ask on their
support channel.

Mark

On Tue, Jun 20, 2017 at 3:21 PM Shivangi Agarwal <
shivangi.agarwal800 at gmail.com> wrote:

> Thanks for your suggestion.
> One more thing
> In topology file generated by ATB, there is HS14 atomtype and i am getting
> error
> FATAL error
> ATomtype HS14 not found
>
> How to handle this error?
> Kindly suggest
>
>
> On Tue, Jun 20, 2017 at 12:18 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > You don't need a file in the gro format. You need coordinates that match
> > the topology present in any supported file format, eg pdb or g96 etc.
> >
> > Mark
> >
> > On Tue, 20 Jun 2017 09:01 Shivangi Agarwal <
> shivangi.agarwal800 at gmail.com>
> > wrote:
> >
> > > Hello
> > >
> > > I used the ATB server for generation of topology file following Gromacs
> > > Turorial
> > >
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> > gmx-tutorials/complex/02_topology.html
> > > <
> > > https://www.researchgate.net/deref/http%3A%2F%2Fwww.
> > bevanlab.biochem.vt.edu%2FPages%2FPersonal%2Fjustin%
> > 2Fgmx-tutorials%2Fcomplex%2F02_topology.html
> > > >
> > >
> > > I need obtain two files .itp & .gro. I used the ATB server.
> > > https://atb.uq.edu.au/molecule.py?molid=225178#panel-md
> > >
> > > The server gave me many files (Topology Files and Structure Files).
> > > I am unable to see my "gro" file.
> > > Please help
> > > Your answer is highly appreciated.
> > > --
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