[gmx-users] topology file

[RAHUL SURESH]

Hey Mark sorry for the inconvenience I have caused you. CYSh file was just
for an example.

And now I have generated the itp file using topolgen.

I would like to run MDS on this particular molecule alone with any protien.

What should I do for that.

Thank you.
On Mon, 23 Jan 2017 at 8:21 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
>
>
> There's not enough information here for anyone to help you (and you can't
>
> attach files to send to the list). Why didn't you find the generated
>
> topologies useful? Why do you care about CYSH?
>
>
>
> Mark
>
>
>
> On Mon, Jan 23, 2017 at 10:46 AM RAHUL SURESH <drrahulsuresh at gmail.com>
>
> wrote:
>
>
>
> > I have tried Ligpargen to generate topology for a molecule and I dont
> find
>
> > it useful. And totally unaware how to use topolgen or topolbuild.
>
> >
>
> > Now I am trying to craft my topology manually. I would like to get some
>
> > guidances.
>
> >
>
> > [ CYSH ]
>
> >  [ atoms ]
>
> >      N    opls_238   -0.500     1
>
> >      H    opls_241    0.300     1
>
> >     CA    opls_224B   0.140     1
>
> >     HA    opls_140    0.060     1
>
> >     CB    opls_206    0.060     2
>
> >    HB1    opls_140    0.060     2
>
> >    HB2    opls_140    0.060     2
>
> >     SG    opls_200   -0.335     3
>
> >     HG    opls_204    0.155     3
>
> >      C    opls_235    0.500     4
>
> >      O    opls_236   -0.500     4
>
> >
>
> > here how to determine these forcefields?
>
> >
>
> >
>
> >
>
> >
>
> > NOTE: I have attached the itp file generated online.
>
> > --
>
> > *Regards,*
>
> > *Rahul Suresh*
>
> > *Research Scholar*
>
> > *Bharathiar University*
>
> > *Coimbatore*
>
> > --
>
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