[gmx-users] topology file

[Justin Lemkul]

On 1/23/17 2:17 PM, RAHUL SURESH wrote:
> Dear Justin
> if I want to run just my ligand, is that possible.?

Sure.  Treat it like any other solute.  You have a topology (that's the hard 
part), so now you just have to solvate it and go using all the normal tools.

-Justin

> On Mon, 23 Jan 2017 at 11:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>>
>>
>> On 1/23/17 12:01 PM, RAHUL SURESH wrote:
>>
>>> 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.
>>
>>>
>>
>>
>>
>> Start with a tutorial to get yourself familiar with protein-ligand systems.
>>
>>
>>
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
>>
>>
>>
>> Also note that a TopolGen topology is based on a lot of assumptions.  You
>> should
>>
>> 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>
>>
>>> 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*
>>
>>>>
>>
>>>>> --
>>
>>>>
>>
>>>>> 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.
>>
>>>>
>>
>>>>
>>
>>
>>
>> --
>>
>> ==================================================
>>
>>
>>
>> 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.
>>
>> Baltimore, MD 21201
>>
>>
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>
>> http://mackerell.umaryland.edu/~jalemkul
>>
>>
>>
>> ==================================================
>>
>> --
>>
>> 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.
>>
>>

-- 
==================================================

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.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================