[gmx-users] adding a custom residue with an itp file

[Jose Borreguero]

Thanks, Justin. I suspected that was the case but I wanted to be 100% sure
:D
.Jose

On Tue, Jun 27, 2017 at 9:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/27/17 12:32 PM, Jose Borreguero wrote:
>
>> Dear Gromacs users,
>>
>> I have created an include topology file (sil.itp) for a silica crystal,
>> but
>> the instructions in
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_
>> Residue_to_a_Force_Field
>> leave me with a couple of unclear points. Please help!
>>
>> 1. This "residue" is not of type 'Protein' or 'DNA', so can I just create
>> a
>> new type in file residuestypes.dat? Something like "SIL Silica"? Do I
>> actually have to declare this molecule within residuestypes.dat?
>>
>> 2. All the bonding info is already in the sil.itp file I just created, but
>> do I still have to include this residue in file aminoacids.rtp?
>>
>>
> You only need aminoacids.rtp and residuetypes.dat if you're running
> pdb2gmx. You already have a topology, so there is no purpose to running
> pdb2gmx.
>
> -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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