[gmx-users] protein-ligand

[RAHUL SURESH]

Yeah. Thank you Mr.Justin

On Tue, Mar 28, 2017 at 7:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/28/17 10:06 AM, RAHUL SURESH wrote:
>
>> But in case of charmm36ff, the script file will not generate .gro file for
>> ligand  I believe. In that case how will i generate gro file?
>>
>>
> I responded to your exact same question yesterday.  Please read that.
>
> -Justin
>
>
> On Tue, Mar 28, 2017 at 5:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 3/27/17 11:49 PM, RAHUL SURESH wrote:
>>>
>>> How will I add ligand .gro file in protein .gro file to make a complex .?
>>>>
>>>>
>>> With a text editor.  Go through my tutorial:
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>>> -tutorials/complex/index.html
>>>
>>> -Justin
>>>
>>>
>>> On Tue, 28 Mar 2017 at 2:12 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>>
>>>>
>>>>
>>>>> On 3/27/17 4:02 PM, RAHUL SURESH wrote:
>>>>>
>>>>> In protein-ligand simulation using charmm36ff, how to generate gro file
>>>>>>
>>>>>> for
>>>>>
>>>>> ligand to add it to the protein gro file?
>>>>>>
>>>>>>
>>>>>> You don't strictly need a .gro file, since GROMACS can handle PDB and
>>>>> other
>>>>> formats, but in short, you can convert between formats easily with
>>>>> editconf.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> 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
>>>>>
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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.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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>>> Gromacs Users mailing list
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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.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*