[gmx-users] topology

[Justin Lemkul]

On 3/27/17 11:51 PM, RAHUL SURESH wrote:
> So it is mandatory to add
>
>> *; Include ligand topology
>> #include "drug.itp"*
>
> In top file.?
>

You can't simulate a drug molecule without telling grompp what it's parameters 
are so that mdrun can simulate it.

-Justin

>
> On Tue, 28 Mar 2017 at 2:08 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/27/17 3:23 PM, RAHUL SURESH wrote:
>>> What if I run my protein-ligand simulation with out using
>>>
>>
>>>
>>> in the topology file generated using pdb2gmx.
>>>
>>> but i have added my ligand in protein.gro file.
>>>
>>
>> Then you'll get a fatal error from grompp about mismatching number of
>> atoms or
>> atom names.
>>
>> -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

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