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

[Justin Lemkul]

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

-- 
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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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