[gmx-users] topology file

[RAHUL SURESH]

Dear Justin
if I want to run just my ligand, is that possible.?
On Mon, 23 Jan 2017 at 11:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
>
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> On 1/23/17 12:01 PM, RAHUL SURESH wrote:
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> > Hey Mark sorry for the inconvenience I have caused you. CYSh file was
> just
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> > for an example.
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> >
>
> > And now I have generated the itp file using topolgen.
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> >
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> > I would like to run MDS on this particular molecule alone with any
> protien.
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> >
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> > What should I do for that.
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> >
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>
>
> Start with a tutorial to get yourself familiar with protein-ligand systems.
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>
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
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>
>
> Also note that a TopolGen topology is based on a lot of assumptions.  You
> should
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> do some basic validation, at least.  See the OPLS-AA papers for the types
> of QM
>
> calculations you should do.
>
>
>
> -Justin
>
>
>
> > Thank you.
>
> > On Mon, 23 Jan 2017 at 8:21 PM, Mark Abraham <mark.j.abraham at gmail.com>
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> > wrote:
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> >
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> >> Hi,
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> >>
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> >>
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> >>
>
> >> There's not enough information here for anyone to help you (and you
> can't
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> >>
>
> >> attach files to send to the list). Why didn't you find the generated
>
> >>
>
> >> topologies useful? Why do you care about CYSH?
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> >>
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> >>
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> >>
>
> >> Mark
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> >>
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> >>
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> >>
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> >> On Mon, Jan 23, 2017 at 10:46 AM RAHUL SURESH <drrahulsuresh at gmail.com>
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> >>
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> >> wrote:
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> >>
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> >>
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> >>
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> >>> 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.
>
> >>
>
> >>>
>
> >>
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> >>> Now I am trying to craft my topology manually. I would like to get some
>
> >>
>
> >>> guidances.
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> >>
>
> >>>
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> >>
>
> >>> [ CYSH ]
>
> >>
>
> >>>  [ atoms ]
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> >>
>
> >>>      N    opls_238   -0.500     1
>
> >>
>
> >>>      H    opls_241    0.300     1
>
> >>
>
> >>>     CA    opls_224B   0.140     1
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> >>
>
> >>>     HA    opls_140    0.060     1
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> >>
>
> >>>     CB    opls_206    0.060     2
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> >>
>
> >>>    HB1    opls_140    0.060     2
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> >>
>
> >>>    HB2    opls_140    0.060     2
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> >>
>
> >>>     SG    opls_200   -0.335     3
>
> >>
>
> >>>     HG    opls_204    0.155     3
>
> >>
>
> >>>      C    opls_235    0.500     4
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> >>
>
> >>>      O    opls_236   -0.500     4
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> >>
>
> >>>
>
> >>
>
> >>> here how to determine these forcefields?
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> >>
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> >>>
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> >>
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> >>>
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> >>
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> >>>
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> >>
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> >>>
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> >>
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> >>> NOTE: I have attached the itp file generated online.
>
> >>
>
> >>> --
>
> >>
>
> >>> *Regards,*
>
> >>
>
> >>> *Rahul Suresh*
>
> >>
>
> >>> *Research Scholar*
>
> >>
>
> >>> *Bharathiar University*
>
> >>
>
> >>> *Coimbatore*
>
> >>
>
> >>> --
>
> >>
>
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>
> >>
>
> >>>
>
> >>
>
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>
> >>
>
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>
> >>
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> >>
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> >>
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> >>
>
> >> --
>
> >>
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> --
>
> ==================================================
>
>
>
> Justin A. Lemkul, Ph.D.
>
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>
>
> Department of Pharmaceutical Sciences
>
> School of Pharmacy
>
> Health Sciences Facility II, Room 629
>
> University of Maryland, Baltimore
>
> 20 Penn St.
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> Baltimore, MD 21201
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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> http://mackerell.umaryland.edu/~jalemkul
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