[gmx-users] protein-ligand

[Justin Lemkul]

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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>> * Please search the archive at http://www.gromacs.org/Support
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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

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