[gmx-users] Ligand hybridization

[Justin Lemkul]

On 7/6/16 12:26 PM, Chetan Puri wrote:
> I am confused with the fact that after processing ligand through prodrg
> whatever pdb file you get it doesn't show aromatic ring double bonds( if we
> view it using pymol or vmd)
> And I don't understand that although it shows aromatic ring planar but no
> double bonds are present.
> So is it the way aromatic ring is supposed to be after passing through
> prodrg.

It has nothing to do with PRODRG (which hopefully you aren't using for 
topologies, unless you're manually correcting them) and everything to do with 
the visualization software.  Most programs don't explicitly render double bonds, 
anyway.

-Justin

> On 5 Jul 2016 10:26 pm, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/5/16 10:50 AM, Chetan Puri wrote:
>>
>>> I am trying to do a protein- ligand simulation.
>>>
>>> And the prodrg server provides the ligand out  put by completely removing
>>> the double bonds(making it saturated)
>>>
>>> So is there any way to do it.
>>>
>>>
>> See the PRODRG FAQ for dealing with incorrect protonation.  Then make sure
>> you fix the PRODRG topology because the charges won't be right.  Or use a
>> better server like ATB.
>>
>> -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

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